A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
This report has been generated by the nf-core/mag analysis pipeline. For information about how to interpret these results, please see the documentation.
/project2/ckenkel_26/liruiqi/Osedax_meta/CR180008_Osedax_frankpressi/work/7d/ede6543f0040a3b52fbb411e7ffdbf
General Statistics
| Sample Name | % Dups (raw) | Mean R1 Length | Mean R2 Length | % GC (raw) | Avg. length (raw) | Median length (raw) | M Seqs (raw) | % Fails (raw) | % Dups (processed) | % GC (processed) | Avg. length (processed) | Median length (processed) | M Seqs (processed) | % Fails (processed) | % Duplication | % > Q30 | Mb Q30 bases | Reads After Filtering | GC content | % PF | % Adapter | % Aligned (PhiX) | % Aligned (Host) | % Aligned (Assem.) | N50 (Kbp) | N50 (Kbp) | Assembly Length (Mbp) | Assembly Length (Mbp) | Complete BUSCOs | Complete and single-copy BUSCOs | Fragmented BUSCOs | Missing BUSCOs | Complete and duplicated BUSCOs | Predicted Completeness | Predicted Contamination | Genome Size | Classification |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| CR180008_O_frankpressi_run0 | 150.0bp | 150.0bp | 13.0% | 95.9% | 6474.3Mb | 45.7M | 33.1% | 99.4% | 3.7% | 0.0% | 73.5% | ||||||||||||||||||||||||||
| CR180008_O_frankpressi_run0_raw_1 | 27.0% | 33.0% | 150bp | 150bp | 23.0M | 0% | |||||||||||||||||||||||||||||||
| CR180008_O_frankpressi_run0_raw_2 | 27.2% | 33.0% | 150bp | 150bp | 23.0M | 9% | |||||||||||||||||||||||||||||||
| CR180008_O_frankpressi_run0_trimmed_1 | 20.2% | 35.0% | 149bp | 150bp | 6.9M | 9% | |||||||||||||||||||||||||||||||
| CR180008_O_frankpressi_run0_trimmed_2 | 20.6% | 36.0% | 149bp | 150bp | 6.9M | 18% | |||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_0 | 1.3Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_1 | 1.6Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_2 | 1.1Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_3 | 1.2Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_4 | 1.3Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_5 | 1.4Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_6 | 1.5Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_7 | 1.0Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_8 | 1.2Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_9 | 1.0Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_10 | 1.1Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_11 | 1.1Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_12 | 1.3Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_13 | 1.2Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_14 | 1.1Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_15 | 1.1Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_16 | 1.2Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_17 | 1.3Kbp | 0.4Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_18 | 1.2Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_19 | 1.0Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_20 | 1.2Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_21 | 1.2Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_22 | 1.6Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_23 | 1.3Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_24 | 1.1Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_25 | 1.2Kbp | 0.1Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_26 | 1.3Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_27 | 1.2Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_28 | 1.3Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_29 | 1.5Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_30 | 1.0Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_31 | 1.2Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_32 | 1.3Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_33 | 1.2Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_34 | 1.2Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_35 | 1.3Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_36 | 1.0Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_37 | 2.7Kbp | 8.5Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_38 | 1.2Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_39 | 1.5Kbp | 9.3Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_40 | 1.2Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_41 | 1.2Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_42 | 1.5Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_43 | 1.2Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_44 | 1.5Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_45 | 1.2Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_46 | 1.1Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_47 | 22.8Kbp | 4.5Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_48 | 1.1Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_49 | 1.4Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_50 | 1.2Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_51 | 2.6Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_52 | 1.8Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_53 | 1.1Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_54 | 1.6Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_55 | 1.3Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_56 | 1.1Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_57 | 1.2Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_58 | 1.3Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_59 | 1.7Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_60 | 1.2Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_61 | 1.1Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_62 | 1.1Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_63 | 1.3Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_64 | 1.1Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_65 | 1.0Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_66 | 1.4Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_67 | 1.1Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_68 | 2.3Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_69 | 1.3Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_70 | 1.4Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_71 | 1.6Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_72 | 1.5Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_73 | 1.2Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_74 | 1.2Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_75 | 1.3Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_76 | 1.3Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_77 | 1.6Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_78 | 1.3Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_79 | 1.2Kbp | 0.3Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_80 | 1.2Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_81 | 1.4Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_82 | 1.3Kbp | 0.1Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_83 | 1.3Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_84 | 2.0Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_85 | 1.2Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_86 | 1.3Kbp | 0.1Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_87 | 1.3Kbp | 0.5Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_88 | 1.2Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_89 | 1.1Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_90 | 1.1Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_91 | 1.1Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_92 | 1.4Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_93 | 3.0Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_94 | 1.3Kbp | 0.1Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_95 | 1.2Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_96 | 1.2Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_97 | 1.3Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_98 | 1.3Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_99 | 1.3Kbp | 0.2Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_100 | 1.2Kbp | 0.1Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_101 | 1.7Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_102 | 2.1Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_103 | 1.1Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_104 | 1.1Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_105 | 1.6Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_106 | 1.3Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_107 | 1.2Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_108 | 1.3Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_109 | 1.3Kbp | 3.6Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_110 | 1.1Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_111 | 1.2Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_112 | 2.1Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_113 | 1.4Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_114 | 1.2Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_115 | 1.7Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_116 | 1.2Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_117 | 1.0Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CONCOCT-CR180008_O_frankpressi_118 | 1.2Kbp | 0.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-CR180008_O_frankpressi | 83.5% | 1.0Kbp | 55.6Mbp | ||||||||||||||||||||||||||||||||||
| SPAdes-MaxBin2-CR180008_O_frankpressi.001 | 22.3Kbp | 4.6Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-MaxBin2-CR180008_O_frankpressi.001.fa | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Pseudomonadales;f__Balneatricaceae;g__Rs1;s__Rs1 sp000416275 | ||||||||||||||||||||||||||||||||||||
| SPAdes-MaxBin2-CR180008_O_frankpressi.002 | 1.6Kbp | 24.0Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-MetaBAT2-CR180008_O_frankpressi.1 | 2.5Kbp | 10.1Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-MetaBAT2-CR180008_O_frankpressi.2 | 22.3Kbp | 3.7Mbp | |||||||||||||||||||||||||||||||||||
| SPAdes-MetaBAT2-CR180008_O_frankpressi.2.fa | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Pseudomonadales;f__Balneatricaceae;g__Rs1;s__Rs1 sp000416275 | ||||||||||||||||||||||||||||||||||||
| SPAdes-SemiBin2-CR180008_O_frankpressi_0 | 22.8Kbp | 4.0Mbp | 89.2% | 1.35% | 4003767 | ||||||||||||||||||||||||||||||||
| SPAdes-SemiBin2-CR180008_O_frankpressi_0.fa | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Pseudomonadales;f__Balneatricaceae;g__Rs1;s__Rs1 sp000416275 | ||||||||||||||||||||||||||||||||||||
| SPAdes-SemiBin2-CR180008_O_frankpressi_1 | 31.5Kbp | 0.2Mbp | 6.2% | 0.00% | 240621 | ||||||||||||||||||||||||||||||||
| SPAdes-SemiBin2-CR180008_O_frankpressi_3 | 3.0Kbp | 1.0Mbp | 5.5% | 0.01% | 956936 | ||||||||||||||||||||||||||||||||
| SPAdes-SemiBin2-CR180008_O_frankpressi_4 | 3.4Kbp | 1.1Mbp | 5.5% | 0.03% | 1129433 | ||||||||||||||||||||||||||||||||
| SPAdes-SemiBin2-CR180008_O_frankpressi_5 | 3.5Kbp | 0.9Mbp | 9.2% | 0.05% | 858658 | ||||||||||||||||||||||||||||||||
| SPAdes-SemiBin2-CR180008_O_frankpressi_6 | 3.2Kbp | 0.4Mbp | 3.2% | 0.00% | 375837 | ||||||||||||||||||||||||||||||||
| SPAdes-SemiBin2-CR180008_O_frankpressi_7 | 3.1Kbp | 1.3Mbp | 5.0% | 0.03% | 1289038 | ||||||||||||||||||||||||||||||||
| SPAdes-SemiBin2-CR180008_O_frankpressi_8 | 2.4Kbp | 1.7Mbp | 19.5% | 6.29% | 1650159 | ||||||||||||||||||||||||||||||||
| SPAdes-SemiBin2-CR180008_O_frankpressi_9 | 2.7Kbp | 1.1Mbp | 6.7% | 0.04% | 1128620 | ||||||||||||||||||||||||||||||||
| SPAdes-SemiBin2-CR180008_O_frankpressi_10 | 2.1Kbp | 0.2Mbp | 2.5% | 0.00% | 230443 | ||||||||||||||||||||||||||||||||
| SPAdes-SemiBin2-CR180008_O_frankpressi_11 | 2.6Kbp | 1.4Mbp | 9.5% | 3.12% | 1436041 | ||||||||||||||||||||||||||||||||
| SPAdes-SemiBin2-CR180008_O_frankpressi_18 | 2.0Kbp | 0.7Mbp | 3.2% | 0.00% | 699504 | ||||||||||||||||||||||||||||||||
| SPAdes-SemiBin2-CR180008_O_frankpressi_22 | 2.1Kbp | 0.3Mbp | 3.5% | 0.00% | 335148 | ||||||||||||||||||||||||||||||||
| SPAdes-SemiBin2-CR180008_O_frankpressi_25 | 1.9Kbp | 0.2Mbp | 3.0% | 0.00% | 229024 | ||||||||||||||||||||||||||||||||
| SPAdes-SemiBin2-CR180008_O_frankpressi_40 | 1.9Kbp | 0.4Mbp | 3.8% | 0.00% | 442141 | ||||||||||||||||||||||||||||||||
| short_summary.generic.bacteria_odb12.SPAdes-MaxBin2-CR180008_O_frankpressi.001 | 114.0 | 113.0 | 0.0 | 2.0 | 1.0 | ||||||||||||||||||||||||||||||||
| short_summary.generic.bacteria_odb12.SPAdes-MetaBAT2-CR180008_O_frankpressi.2 | 96.0 | 95.0 | 1.0 | 19.0 | 1.0 | ||||||||||||||||||||||||||||||||
| short_summary.specific.eukaryota_odb12.SPAdes-MaxBin2-CR180008_O_frankpressi.002 | 0.0 | 0.0 | 10.0 | 119.0 | 0.0 | ||||||||||||||||||||||||||||||||
| short_summary.specific.eukaryota_odb12.SPAdes-MetaBAT2-CR180008_O_frankpressi.1 | 0.0 | 0.0 | 3.0 | 126.0 | 0.0 | ||||||||||||||||||||||||||||||||
| short_summary.specific.oceanospirillaceae_odb12.SPAdes-MaxBin2-CR180008_O_frankpressi.001 | 716.0 | 714.0 | 5.0 | 41.0 | 2.0 | ||||||||||||||||||||||||||||||||
| short_summary.specific.oceanospirillaceae_odb12.SPAdes-MetaBAT2-CR180008_O_frankpressi.2 | 628.0 | 626.0 | 4.0 | 130.0 | 2.0 |
FastQC: raw reads
Quality control tool for high throughput sequencing data.URL: http://www.bioinformatics.babraham.ac.uk/projects/fastqc
Sequence Counts
Sequence counts for each sample. Duplicate read counts are an estimate only.
This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).
You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:
Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.
The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.
Sequence Quality Histograms
The mean quality value across each base position in the read.
To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).
Taken from the FastQC help:
The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.
Per Sequence Quality Scores
The number of reads with average quality scores. Shows if a subset of reads has poor quality.
From the FastQC help:
The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.
Per Base Sequence Content
The proportion of each base position for which each of the four normal DNA bases has been called.
To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.
To see the data as a line plot, as in the original FastQC graph, click on a sample track.
From the FastQC help:
Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.
In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.
It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.
Rollover for sample name
Per Sequence GC Content
The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.
From the FastQC help:
This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.
In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.
An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.
Per Base N Content
The percentage of base calls at each position for which an N was called.
From the FastQC help:
If a sequencer is unable to make a base call with sufficient confidence then it will
normally substitute an N rather than a conventional base call. This graph shows the
percentage of base calls at each position for which an N was called.
It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.
Sequence Length Distribution
Sequence Duplication Levels
The relative level of duplication found for every sequence.
From the FastQC Help:
In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (e.g. PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.
Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.
The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.
In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.
Overrepresented sequences by sample
The total amount of overrepresented sequences found in each library.
FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as overrepresented.
Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.
From the FastQC Help:
A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.
FastQC lists all the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.
Top overrepresented sequences
Top overrepresented sequences across all samples. The table shows 20 most overrepresented sequences across all samples, ranked by the number of samples they occur in.
| Overrepresented sequence | Reports | Occurrences | % of all reads |
|---|---|---|---|
| GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG | 1 | 40096 | 0.0873% |
Adapter Content
The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.
Note that only samples with ≥ 0.1% adapter contamination are shown.
There may be several lines per sample, as one is shown for each adapter detected in the file.
From the FastQC Help:
The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.
Status Checks
Status for each FastQC section showing whether results seem entirely normal (green), slightly abnormal (orange) or very unusual (red).
FastQC assigns a status for each section of the report. These give a quick evaluation of whether the results of the analysis seem entirely normal (green), slightly abnormal (orange) or very unusual (red).
It is important to stress that although the analysis results appear to give a pass/fail result, these evaluations must be taken in the context of what you expect from your library. A 'normal' sample as far as FastQC is concerned is random and diverse. Some experiments may be expected to produce libraries which are biased in particular ways. You should treat the summary evaluations therefore as pointers to where you should concentrate your attention and understand why your library may not look random and diverse.
Specific guidance on how to interpret the output of each module can be found in the relevant report section, or in the FastQC help.
In this heatmap, we summarise all of these into a single heatmap for a quick overview. Note that not all FastQC sections have plots in MultiQC reports, but all status checks are shown in this heatmap.
fastp
All-in-one FASTQ preprocessor (QC, adapters, trimming, filtering, splitting...).URL: https://github.com/OpenGene/fastpDOI: 10.1093/bioinformatics/bty560
Fastp goes through fastq files in a folder and perform a series of quality control and filtering. Quality control and reporting are displayed both before and after filtering, allowing for a clear depiction of the consequences of the filtering process. Notably, the latter can be conducted on a variety of parameters including quality scores, length, as well as the presence of adapters, polyG, or polyX tailing.Filtered Reads
Filtering statistics of sampled reads.
Insert Sizes
Insert size estimation of sampled reads.
Sequence Quality
Average sequencing quality over each base of all reads.
GC Content
Average GC content over each base of all reads.
N content
Average N content over each base of all reads.
FastQC: after preprocessing
After trimming and, if requested, contamination removal.URL: http://www.bioinformatics.babraham.ac.uk/projects/fastqc
Sequence Counts
Sequence counts for each sample. Duplicate read counts are an estimate only.
This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).
You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:
Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.
The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.
Sequence Quality Histograms
The mean quality value across each base position in the read.
To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).
Taken from the FastQC help:
The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.
Per Sequence Quality Scores
The number of reads with average quality scores. Shows if a subset of reads has poor quality.
From the FastQC help:
The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.
Per Base Sequence Content
The proportion of each base position for which each of the four normal DNA bases has been called.
To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.
To see the data as a line plot, as in the original FastQC graph, click on a sample track.
From the FastQC help:
Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.
In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.
It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.
Rollover for sample name
Per Sequence GC Content
The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.
From the FastQC help:
This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.
In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.
An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.
Per Base N Content
The percentage of base calls at each position for which an N was called.
From the FastQC help:
If a sequencer is unable to make a base call with sufficient confidence then it will
normally substitute an N rather than a conventional base call. This graph shows the
percentage of base calls at each position for which an N was called.
It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.
Sequence Length Distribution
The distribution of fragment sizes (read lengths) found. See the FastQC help
Sequence Duplication Levels
The relative level of duplication found for every sequence.
From the FastQC Help:
In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (e.g. PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.
Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.
The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.
In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.
Overrepresented sequences by sample
The total amount of overrepresented sequences found in each library.
FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as overrepresented.
Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.
From the FastQC Help:
A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.
FastQC lists all the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.
Top overrepresented sequences
Top overrepresented sequences across all samples. The table shows 20 most overrepresented sequences across all samples, ranked by the number of samples they occur in.
| Overrepresented sequence | Reports | Occurrences | % of all reads |
|---|---|---|---|
| GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG | 1 | 36879 | 0.2688% |
Adapter Content
The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.
Note that only samples with ≥ 0.1% adapter contamination are shown.
There may be several lines per sample, as one is shown for each adapter detected in the file.
From the FastQC Help:
The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.
Status Checks
Status for each FastQC section showing whether results seem entirely normal (green), slightly abnormal (orange) or very unusual (red).
FastQC assigns a status for each section of the report. These give a quick evaluation of whether the results of the analysis seem entirely normal (green), slightly abnormal (orange) or very unusual (red).
It is important to stress that although the analysis results appear to give a pass/fail result, these evaluations must be taken in the context of what you expect from your library. A 'normal' sample as far as FastQC is concerned is random and diverse. Some experiments may be expected to produce libraries which are biased in particular ways. You should treat the summary evaluations therefore as pointers to where you should concentrate your attention and understand why your library may not look random and diverse.
Specific guidance on how to interpret the output of each module can be found in the relevant report section, or in the FastQC help.
In this heatmap, we summarise all of these into a single heatmap for a quick overview. Note that not all FastQC sections have plots in MultiQC reports, but all status checks are shown in this heatmap.
Bowtie2: PhiX removal
Mapping statistics of reads mapped against PhiX and subsequently removed.URL: http://bowtie-bio.sourceforge.net/bowtie2; https://ccb.jhu.edu/software/hisat2DOI: 10.1038/nmeth.1923; 10.1038/nmeth.3317; 10.1038/s41587-019-0201-4
Paired-end alignments
This plot shows the number of reads aligning to the reference in different ways.
There are 6 possible types of alignment:
- PE mapped uniquely: Pair has only one occurence in the reference genome.
- PE mapped discordantly uniquely: Pair has only one occurence but not in proper pair.
- PE one mate mapped uniquely: One read of a pair has one occurence.
- PE multimapped: Pair has multiple occurence.
- PE one mate multimapped: One read of a pair has multiple occurence.
- PE neither mate aligned: Pair has no occurence.
Bowtie2: host removal
Mapping statistics of reads mapped against host genome and subsequently removed.URL: http://bowtie-bio.sourceforge.net/bowtie2; https://ccb.jhu.edu/software/hisat2DOI: 10.1038/nmeth.1923; 10.1038/nmeth.3317; 10.1038/s41587-019-0201-4
Paired-end alignments
This plot shows the number of reads aligning to the reference in different ways.
There are 6 possible types of alignment:
- PE mapped uniquely: Pair has only one occurence in the reference genome.
- PE mapped discordantly uniquely: Pair has only one occurence but not in proper pair.
- PE one mate mapped uniquely: One read of a pair has one occurence.
- PE multimapped: Pair has multiple occurence.
- PE one mate multimapped: One read of a pair has multiple occurence.
- PE neither mate aligned: Pair has no occurence.
QUAST: assembly
Assembly statistics of raw assemblies.URL: http://quast.bioinf.spbau.ruDOI: 10.1093/bioinformatics/btt086
Assembly Statistics
| Sample Name | N50 (Kbp) | N75 (Kbp) | L50 (K) | L75 (K) | Largest contig (Kbp) | Length (Mbp) |
|---|---|---|---|---|---|---|
| SPAdes-CR180008_O_frankpressi | 1.0Kbp | 0.7Kbp | 14.0K | 30.9K | 110.7Kbp | 55.6Mbp |
Number of Contigs
This plot shows the number of contigs found for each assembly, broken down by length.
Bowtie2: assembly
Mapping statistics of reads mapped against assemblies.URL: http://bowtie-bio.sourceforge.net/bowtie2; https://ccb.jhu.edu/software/hisat2DOI: 10.1038/nmeth.1923; 10.1038/nmeth.3317; 10.1038/s41587-019-0201-4
Paired-end alignments
This plot shows the number of reads aligning to the reference in different ways.
There are 6 possible types of alignment:
- PE mapped uniquely: Pair has only one occurence in the reference genome.
- PE mapped discordantly uniquely: Pair has only one occurence but not in proper pair.
- PE one mate mapped uniquely: One read of a pair has one occurence.
- PE multimapped: Pair has multiple occurence.
- PE one mate multimapped: One read of a pair has multiple occurence.
- PE neither mate aligned: Pair has no occurence.
QUAST: bins
Assembly statistics of binned assemblies.URL: http://quast.bioinf.spbau.ruDOI: 10.1093/bioinformatics/btt086
Assembly Statistics
| Sample Name | N50 (Kbp) | N75 (Kbp) | L50 (K) | L75 (K) | Largest contig (Kbp) | Length (Mbp) |
|---|---|---|---|---|---|---|
| SPAdes-CONCOCT-CR180008_O_frankpressi_0 | 1.3Kbp | 1.1Kbp | 0.0K | 0.0K | 2.3Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_1 | 1.6Kbp | 1.3Kbp | 0.0K | 0.0K | 3.1Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_2 | 1.1Kbp | 1.0Kbp | 0.0K | 0.0K | 1.7Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_3 | 1.2Kbp | 1.2Kbp | 0.0K | 0.0K | 1.6Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_4 | 1.3Kbp | 1.1Kbp | 0.0K | 0.0K | 2.1Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_5 | 1.4Kbp | 1.3Kbp | 0.0K | 0.0K | 2.0Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_6 | 1.5Kbp | 1.5Kbp | 0.0K | 0.0K | 1.5Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_7 | 1.0Kbp | 1.0Kbp | 0.0K | 0.0K | 1.0Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_8 | 1.2Kbp | 1.1Kbp | 0.0K | 0.0K | 1.8Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_9 | 1.0Kbp | 1.0Kbp | 0.0K | 0.0K | 1.0Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_10 | 1.1Kbp | 1.1Kbp | 0.0K | 0.0K | 1.8Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_11 | 1.1Kbp | 1.1Kbp | 0.0K | 0.0K | 1.9Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_12 | 1.3Kbp | 1.2Kbp | 0.0K | 0.0K | 2.1Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_13 | 1.2Kbp | 1.1Kbp | 0.0K | 0.0K | 2.4Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_14 | 1.1Kbp | 1.1Kbp | 0.0K | 0.0K | 1.1Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_15 | 1.1Kbp | 1.1Kbp | 0.0K | 0.0K | 1.1Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_16 | 1.2Kbp | 1.1Kbp | 0.0K | 0.0K | 1.2Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_17 | 1.3Kbp | 1.1Kbp | 0.1K | 0.2K | 4.0Kbp | 0.4Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_18 | 1.2Kbp | 1.1Kbp | 0.0K | 0.0K | 2.1Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_19 | 1.0Kbp | 1.0Kbp | 0.0K | 0.0K | 1.0Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_20 | 1.2Kbp | 1.1Kbp | 0.0K | 0.0K | 1.2Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_21 | 1.2Kbp | 1.1Kbp | 0.0K | 0.0K | 1.2Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_22 | 1.6Kbp | 1.2Kbp | 0.0K | 0.0K | 1.6Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_23 | 1.3Kbp | 1.1Kbp | 0.0K | 0.0K | 1.5Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_24 | 1.1Kbp | 1.1Kbp | 0.0K | 0.0K | 1.1Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_25 | 1.2Kbp | 1.1Kbp | 0.0K | 0.0K | 2.7Kbp | 0.1Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_26 | 1.3Kbp | 1.1Kbp | 0.0K | 0.0K | 1.5Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_27 | 1.2Kbp | 1.2Kbp | 0.0K | 0.0K | 1.2Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_28 | 1.3Kbp | 1.2Kbp | 0.0K | 0.0K | 1.5Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_29 | 1.5Kbp | 1.5Kbp | 0.0K | 0.0K | 1.5Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_30 | 1.0Kbp | 1.0Kbp | 0.0K | 0.0K | 1.0Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_31 | 1.2Kbp | 1.1Kbp | 0.0K | 0.0K | 1.6Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_32 | 1.3Kbp | 1.1Kbp | 0.0K | 0.0K | 1.5Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_33 | 1.2Kbp | 1.1Kbp | 0.0K | 0.0K | 1.9Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_34 | 1.2Kbp | 1.2Kbp | 0.0K | 0.0K | 1.2Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_35 | 1.3Kbp | 1.2Kbp | 0.0K | 0.0K | 1.5Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_36 | 1.0Kbp | 1.0Kbp | 0.0K | 0.0K | 1.0Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_37 | 2.7Kbp | 1.9Kbp | 1.1K | 2.0K | 12.2Kbp | 8.5Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_38 | 1.2Kbp | 1.1Kbp | 0.0K | 0.0K | 1.5Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_39 | 1.5Kbp | 1.2Kbp | 2.4K | 4.1K | 6.8Kbp | 9.3Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_40 | 1.2Kbp | 1.0Kbp | 0.0K | 0.0K | 2.2Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_41 | 1.2Kbp | 1.2Kbp | 0.0K | 0.0K | 1.2Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_42 | 1.5Kbp | 1.0Kbp | 0.0K | 0.0K | 1.5Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_43 | 1.2Kbp | 1.2Kbp | 0.0K | 0.0K | 1.2Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_44 | 1.5Kbp | 1.1Kbp | 0.0K | 0.0K | 2.5Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_45 | 1.2Kbp | 1.1Kbp | 0.0K | 0.0K | 2.0Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_46 | 1.1Kbp | 1.0Kbp | 0.0K | 0.0K | 1.2Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_47 | 22.8Kbp | 12.0Kbp | 0.1K | 0.1K | 110.7Kbp | 4.5Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_48 | 1.1Kbp | 1.1Kbp | 0.0K | 0.0K | 1.4Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_49 | 1.4Kbp | 1.2Kbp | 0.0K | 0.0K | 1.6Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_50 | 1.2Kbp | 1.1Kbp | 0.0K | 0.0K | 1.9Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_51 | 2.6Kbp | 2.6Kbp | 0.0K | 0.0K | 2.6Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_52 | 1.8Kbp | 1.2Kbp | 0.0K | 0.0K | 1.8Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_53 | 1.1Kbp | 1.1Kbp | 0.0K | 0.0K | 1.1Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_54 | 1.6Kbp | 1.3Kbp | 0.0K | 0.0K | 1.6Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_55 | 1.3Kbp | 1.1Kbp | 0.0K | 0.0K | 2.0Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_56 | 1.1Kbp | 1.1Kbp | 0.0K | 0.0K | 2.1Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_57 | 1.2Kbp | 1.1Kbp | 0.0K | 0.0K | 1.6Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_58 | 1.3Kbp | 1.1Kbp | 0.0K | 0.0K | 2.0Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_59 | 1.7Kbp | 1.5Kbp | 0.0K | 0.0K | 1.7Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_60 | 1.2Kbp | 1.2Kbp | 0.0K | 0.0K | 1.2Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_61 | 1.1Kbp | 1.1Kbp | 0.0K | 0.0K | 1.1Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_62 | 1.1Kbp | 1.1Kbp | 0.0K | 0.0K | 1.8Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_63 | 1.3Kbp | 1.2Kbp | 0.0K | 0.0K | 2.6Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_64 | 1.1Kbp | 1.0Kbp | 0.0K | 0.0K | 1.2Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_65 | 1.0Kbp | 1.0Kbp | 0.0K | 0.0K | 1.0Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_66 | 1.4Kbp | 1.2Kbp | 0.0K | 0.0K | 2.2Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_67 | 1.1Kbp | 1.1Kbp | 0.0K | 0.0K | 1.7Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_68 | 2.3Kbp | 1.1Kbp | 0.0K | 0.0K | 2.3Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_69 | 1.3Kbp | 1.2Kbp | 0.0K | 0.0K | 2.1Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_70 | 1.4Kbp | 1.3Kbp | 0.0K | 0.0K | 1.4Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_71 | 1.6Kbp | 1.2Kbp | 0.0K | 0.0K | 3.0Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_72 | 1.5Kbp | 1.1Kbp | 0.0K | 0.0K | 3.1Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_73 | 1.2Kbp | 1.1Kbp | 0.0K | 0.0K | 2.3Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_74 | 1.2Kbp | 1.1Kbp | 0.0K | 0.0K | 1.8Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_75 | 1.3Kbp | 1.1Kbp | 0.0K | 0.0K | 3.2Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_76 | 1.3Kbp | 1.1Kbp | 0.0K | 0.0K | 3.7Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_77 | 1.6Kbp | 1.6Kbp | 0.0K | 0.0K | 1.6Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_78 | 1.3Kbp | 1.1Kbp | 0.0K | 0.0K | 1.4Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_79 | 1.2Kbp | 1.1Kbp | 0.1K | 0.1K | 2.7Kbp | 0.3Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_80 | 1.2Kbp | 1.2Kbp | 0.0K | 0.0K | 1.9Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_81 | 1.4Kbp | 1.3Kbp | 0.0K | 0.0K | 1.4Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_82 | 1.3Kbp | 1.1Kbp | 0.0K | 0.0K | 2.9Kbp | 0.1Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_83 | 1.3Kbp | 1.1Kbp | 0.0K | 0.0K | 1.3Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_84 | 2.0Kbp | 2.0Kbp | 0.0K | 0.0K | 2.0Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_85 | 1.2Kbp | 1.1Kbp | 0.0K | 0.0K | 3.0Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_86 | 1.3Kbp | 1.2Kbp | 0.0K | 0.0K | 3.0Kbp | 0.1Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_87 | 1.3Kbp | 1.1Kbp | 0.1K | 0.2K | 4.2Kbp | 0.5Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_88 | 1.2Kbp | 1.1Kbp | 0.0K | 0.0K | 1.5Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_89 | 1.1Kbp | 1.0Kbp | 0.0K | 0.0K | 1.6Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_90 | 1.1Kbp | 1.1Kbp | 0.0K | 0.0K | 1.1Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_91 | 1.1Kbp | 1.0Kbp | 0.0K | 0.0K | 1.8Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_92 | 1.4Kbp | 1.2Kbp | 0.0K | 0.0K | 2.6Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_93 | 3.0Kbp | 1.3Kbp | 0.0K | 0.0K | 5.3Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_94 | 1.3Kbp | 1.1Kbp | 0.0K | 0.0K | 2.4Kbp | 0.1Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_95 | 1.2Kbp | 1.2Kbp | 0.0K | 0.0K | 1.8Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_96 | 1.2Kbp | 1.1Kbp | 0.0K | 0.0K | 1.7Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_97 | 1.3Kbp | 1.1Kbp | 0.0K | 0.0K | 2.2Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_98 | 1.3Kbp | 1.1Kbp | 0.0K | 0.0K | 2.8Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_99 | 1.3Kbp | 1.1Kbp | 0.0K | 0.1K | 3.1Kbp | 0.2Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_100 | 1.2Kbp | 1.1Kbp | 0.0K | 0.0K | 2.0Kbp | 0.1Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_101 | 1.7Kbp | 1.3Kbp | 0.0K | 0.0K | 2.2Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_102 | 2.1Kbp | 1.7Kbp | 0.0K | 0.0K | 2.1Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_103 | 1.1Kbp | 1.1Kbp | 0.0K | 0.0K | 1.6Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_104 | 1.1Kbp | 1.0Kbp | 0.0K | 0.0K | 1.2Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_105 | 1.6Kbp | 1.4Kbp | 0.0K | 0.0K | 1.6Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_106 | 1.3Kbp | 1.1Kbp | 0.0K | 0.0K | 1.3Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_107 | 1.2Kbp | 1.0Kbp | 0.0K | 0.0K | 2.3Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_108 | 1.3Kbp | 1.3Kbp | 0.0K | 0.0K | 1.8Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_109 | 1.3Kbp | 1.1Kbp | 1.0K | 1.7K | 5.2Kbp | 3.6Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_110 | 1.1Kbp | 1.1Kbp | 0.0K | 0.0K | 1.1Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_111 | 1.2Kbp | 1.1Kbp | 0.0K | 0.0K | 2.1Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_112 | 2.1Kbp | 2.1Kbp | 0.0K | 0.0K | 2.1Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_113 | 1.4Kbp | 1.4Kbp | 0.0K | 0.0K | 1.4Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_114 | 1.2Kbp | 1.1Kbp | 0.0K | 0.0K | 1.8Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_115 | 1.7Kbp | 1.7Kbp | 0.0K | 0.0K | 1.7Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_116 | 1.2Kbp | 1.2Kbp | 0.0K | 0.0K | 1.2Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_117 | 1.0Kbp | 1.0Kbp | 0.0K | 0.0K | 1.0Kbp | 0.0Mbp |
| SPAdes-CONCOCT-CR180008_O_frankpressi_118 | 1.2Kbp | 1.1Kbp | 0.0K | 0.0K | 1.5Kbp | 0.0Mbp |
| SPAdes-MaxBin2-CR180008_O_frankpressi.001 | 22.3Kbp | 11.5Kbp | 0.1K | 0.1K | 110.7Kbp | 4.6Mbp |
| SPAdes-MaxBin2-CR180008_O_frankpressi.002 | 1.6Kbp | 1.2Kbp | 4.7K | 8.9K | 12.2Kbp | 24.0Mbp |
| SPAdes-MetaBAT2-CR180008_O_frankpressi.1 | 2.5Kbp | 1.9Kbp | 1.4K | 2.6K | 12.2Kbp | 10.1Mbp |
| SPAdes-MetaBAT2-CR180008_O_frankpressi.2 | 22.3Kbp | 12.6Kbp | 0.1K | 0.1K | 110.7Kbp | 3.7Mbp |
| SPAdes-SemiBin2-CR180008_O_frankpressi_0 | 22.8Kbp | 13.3Kbp | 0.1K | 0.1K | 110.7Kbp | 4.0Mbp |
| SPAdes-SemiBin2-CR180008_O_frankpressi_1 | 31.5Kbp | 14.8Kbp | 0.0K | 0.0K | 46.4Kbp | 0.2Mbp |
| SPAdes-SemiBin2-CR180008_O_frankpressi_3 | 3.0Kbp | 2.1Kbp | 0.1K | 0.2K | 12.2Kbp | 1.0Mbp |
| SPAdes-SemiBin2-CR180008_O_frankpressi_4 | 3.4Kbp | 2.5Kbp | 0.1K | 0.2K | 9.7Kbp | 1.1Mbp |
| SPAdes-SemiBin2-CR180008_O_frankpressi_5 | 3.5Kbp | 2.4Kbp | 0.1K | 0.2K | 9.4Kbp | 0.9Mbp |
| SPAdes-SemiBin2-CR180008_O_frankpressi_6 | 3.2Kbp | 2.4Kbp | 0.0K | 0.1K | 8.6Kbp | 0.4Mbp |
| SPAdes-SemiBin2-CR180008_O_frankpressi_7 | 3.1Kbp | 2.3Kbp | 0.2K | 0.3K | 8.3Kbp | 1.3Mbp |
| SPAdes-SemiBin2-CR180008_O_frankpressi_8 | 2.4Kbp | 1.9Kbp | 0.2K | 0.4K | 7.8Kbp | 1.7Mbp |
| SPAdes-SemiBin2-CR180008_O_frankpressi_9 | 2.7Kbp | 2.2Kbp | 0.2K | 0.3K | 7.6Kbp | 1.1Mbp |
| SPAdes-SemiBin2-CR180008_O_frankpressi_10 | 2.1Kbp | 1.8Kbp | 0.0K | 0.1K | 7.0Kbp | 0.2Mbp |
| SPAdes-SemiBin2-CR180008_O_frankpressi_11 | 2.6Kbp | 2.1Kbp | 0.2K | 0.4K | 7.0Kbp | 1.4Mbp |
| SPAdes-SemiBin2-CR180008_O_frankpressi_18 | 2.0Kbp | 1.7Kbp | 0.1K | 0.2K | 4.9Kbp | 0.7Mbp |
| SPAdes-SemiBin2-CR180008_O_frankpressi_22 | 2.1Kbp | 1.8Kbp | 0.1K | 0.1K | 4.6Kbp | 0.3Mbp |
| SPAdes-SemiBin2-CR180008_O_frankpressi_25 | 1.9Kbp | 1.7Kbp | 0.0K | 0.1K | 4.5Kbp | 0.2Mbp |
| SPAdes-SemiBin2-CR180008_O_frankpressi_40 | 1.9Kbp | 1.7Kbp | 0.1K | 0.2K | 3.7Kbp | 0.4Mbp |
Number of Contigs
This plot shows the number of contigs found for each assembly, broken down by length.
BUSCO
BUSCO assesses genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs. In case BUSCO's automated lineage selection was used, only generic results for the selected domain are shown and only for genome bins and kept, unbinned contigs for which the BUSCO analysis was successfull, i.e. not for contigs for which no BUSCO genes could be found. Bins for which a specific virus lineage was selected are also not shown.URL: http://busco.ezlab.orgDOI: 10.1093/bioinformatics/btv351
BUSCO v2 provides quantitative measures for the assessment of genome assembly, gene set, and transcriptome completeness, based on evolutionarily-informed expectations of gene content from near-universal single-copy orthologs selected from OrthoDB v9.Lineage: eukaryota_odb12
Lineage: bacteria_odb12
Lineage: oceanospirillaceae_odb12
CheckM2
Assesses microbial genome quality using machine learning.URL: https://github.com/chklovski/CheckM2DOI: 10.1038/s41592-023-01940-w
Bin quality
Rapid assessment of genome bin quality using machine learning.
The main use of CheckM2 is to predict the completeness and contamination of metagenome-assembled genomes (MAGs) and single-amplified genomes (SAGs), although it can also be applied to isolate genomes.
| Sample Name | Predicted Completeness | Predicted Contamination | Completeness Model Used | Translation Table Used | Coding Density | Contig N50 | Average Gene Length | Genome Size | GC Content | Total Coding Sequences | Total Contigs | Max Contig Length |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| SPAdes-SemiBin2-CR180008_O_frankpressi_0 | 89.2% | 1.35% | Gradient Boost (General Model) | 11 | 0.806 | 22780 | 302a.a. | 4003767 | 0.44 | 3567 | 265 | 110737 |
| SPAdes-SemiBin2-CR180008_O_frankpressi_1 | 6.2% | 0.00% | Neural Network (Specific Model) | 11 | 0.847 | 31475 | 313a.a. | 240621 | 0.46 | 217 | 12 | 46388 |
| SPAdes-SemiBin2-CR180008_O_frankpressi_3 | 5.5% | 0.01% | Neural Network (Specific Model) | 11 | 0.192 | 2966 | 74a.a. | 956936 | 0.25 | 834 | 343 | 12212 |
| SPAdes-SemiBin2-CR180008_O_frankpressi_4 | 5.5% | 0.03% | Neural Network (Specific Model) | 11 | 0.162 | 3353 | 69a.a. | 1129433 | 0.28 | 893 | 365 | 9651 |
| SPAdes-SemiBin2-CR180008_O_frankpressi_5 | 9.2% | 0.05% | Neural Network (Specific Model) | 11 | 0.297 | 3451 | 78a.a. | 858658 | 0.30 | 1113 | 273 | 9443 |
| SPAdes-SemiBin2-CR180008_O_frankpressi_6 | 3.2% | 0.00% | Neural Network (Specific Model) | 11 | 0.219 | 3156 | 79a.a. | 375837 | 0.31 | 352 | 126 | 8566 |
| SPAdes-SemiBin2-CR180008_O_frankpressi_7 | 5.0% | 0.03% | Neural Network (Specific Model) | 11 | 0.121 | 3126 | 67a.a. | 1289038 | 0.22 | 788 | 441 | 8322 |
| SPAdes-SemiBin2-CR180008_O_frankpressi_8 | 19.5% | 6.29% | Neural Network (Specific Model) | 11 | 0.390 | 2382 | 92a.a. | 1650159 | 0.38 | 2350 | 689 | 7806 |
| SPAdes-SemiBin2-CR180008_O_frankpressi_9 | 6.7% | 0.04% | Neural Network (Specific Model) | 11 | 0.183 | 2657 | 63a.a. | 1128620 | 0.25 | 1115 | 433 | 7565 |
| SPAdes-SemiBin2-CR180008_O_frankpressi_10 | 2.5% | 0.00% | Neural Network (Specific Model) | 11 | 0.132 | 2091 | 73a.a. | 230443 | 0.29 | 140 | 105 | 6976 |
| SPAdes-SemiBin2-CR180008_O_frankpressi_11 | 9.5% | 3.12% | Neural Network (Specific Model) | 11 | 0.241 | 2648 | 71a.a. | 1436041 | 0.31 | 1643 | 550 | 6972 |
| SPAdes-SemiBin2-CR180008_O_frankpressi_18 | 3.2% | 0.00% | Neural Network (Specific Model) | 11 | 0.089 | 1964 | 57a.a. | 699504 | 0.20 | 368 | 349 | 4881 |
| SPAdes-SemiBin2-CR180008_O_frankpressi_22 | 3.5% | 0.00% | Neural Network (Specific Model) | 11 | 0.217 | 2092 | 63a.a. | 335148 | 0.30 | 399 | 159 | 4610 |
| SPAdes-SemiBin2-CR180008_O_frankpressi_25 | 3.0% | 0.00% | Neural Network (Specific Model) | 11 | 0.294 | 1913 | 83a.a. | 229024 | 0.36 | 271 | 113 | 4497 |
| SPAdes-SemiBin2-CR180008_O_frankpressi_40 | 3.8% | 0.00% | Neural Network (Specific Model) | 11 | 0.186 | 1920 | 58a.a. | 442141 | 0.25 | 483 | 228 | 3682 |
GTDB-Tk
Assigns objective taxonomic classifications to bacterial and archaeal genomes.URL: https://ecogenomics.github.io/GTDBTk/index.htmlDOI: 10.1093/bioinformatics/btac672
MAG taxonomy
The taxonomy of a MAG as found by GTDB.
GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds or thousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can also be applied to isolate and single-cell genomes.
| User genome | Classification | Full classification | Classification method | ANI to closest genome | AF to closest genome | RED | Warnings | Notes |
|---|---|---|---|---|---|---|---|---|
| SPAdes-MaxBin2-CR180008_O_frankpressi.001.fa | s__Rs1 sp000416275 | d__Bacteria; p__Pseudomonadota; c__Gammaproteobacteria; o__Pseudomonadales; f__Balneatricaceae; g__Rs1; s__Rs1 sp000416275 | ani_screen | 96.8 | 0.8 | classification based on ANI only | ||
| SPAdes-MetaBAT2-CR180008_O_frankpressi.2.fa | s__Rs1 sp000416275 | d__Bacteria; p__Pseudomonadota; c__Gammaproteobacteria; o__Pseudomonadales; f__Balneatricaceae; g__Rs1; s__Rs1 sp000416275 | ani_screen | 96.8 | 0.8 | classification based on ANI only | ||
| SPAdes-SemiBin2-CR180008_O_frankpressi_0.fa | s__Rs1 sp000416275 | d__Bacteria; p__Pseudomonadota; c__Gammaproteobacteria; o__Pseudomonadales; f__Balneatricaceae; g__Rs1; s__Rs1 sp000416275 | ani_screen | 96.9 | 0.8 | classification based on ANI only |
Software Versions
Software Versions lists versions of software tools extracted from file contents.
| Group | Software | Version |
|---|---|---|
| ADJUST_MAXBIN2_EXT | coreutils | 9.5 |
| ALE | ale | 20180904 |
| BIN_SUMMARY | pandas | 1.4.3 |
| python | 3.10.6 | |
| BOWTIE2_ASSEMBLY_ALIGN | bowtie2 | 2.4.2 |
| pigz | 2.3.4 | |
| samtools | 1.11 | |
| BOWTIE2_ASSEMBLY_BUILD | bowtie2 | 2.4.2 |
| BOWTIE2_HOST_REMOVAL_ALIGN | bowtie2 | 2.4.2 |
| BOWTIE2_HOST_REMOVAL_BUILD | bowtie2 | 2.4.2 |
| BOWTIE2_PHIX_REMOVAL_ALIGN | bowtie2 | 2.4.2 |
| BOWTIE2_PHIX_REMOVAL_BUILD | bowtie2 | 2.4.2 |
| BUSCO_BUSCO | busco | 6.0.0 |
| CHECKM2_PREDICT | checkm2 | 1.1.0 |
| CHECKM2_UNTAR | untar | 1.34 |
| CONCAT_BUSCO_TSV | qsv | 5.1.0 |
| CONCAT_CHECKM2_TSV | qsv | 5.1.0 |
| CONCOCT_CONCOCT | concoct | 1.1.0 |
| CONCOCT_CONCOCTCOVERAGETABLE | concoct | 1.1.0 |
| CONCOCT_CUTUPFASTA | concoct | 1.1.0 |
| CONCOCT_EXTRACTFASTABINS | concoct | 1.1.0 |
| CONCOCT_MERGECUTUPCLUSTERING | concoct | 1.1.0 |
| CONVERT_DEPTHS | bioawk | 20110810 |
| FASTQC_RAW | fastqc | 0.12.1 |
| FASTQC_TRIMMED | fastqc | 0.12.1 |
| GTDBTK_CLASSIFYWF | gtdb_db | r226 |
| gtdbtk | 2.5.2 | |
| GTDBTK_SUMMARY | pandas | 1.4.3 |
| python | 3.10.6 | |
| GUNZIP_BINS | gunzip | 1.13 |
| GUNZIP_SHORTREAD_ASSEMBLIES | gunzip | 1.13 |
| MAG_DEPTHS | pandas | 1.1.5 |
| python | 3.6.7 | |
| MAG_DEPTHS_SUMMARY | pandas | 1.4.3 |
| python | 3.10.6 | |
| MAXBIN2 | maxbin2 | 2.2.7 |
| METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS_SHORTREAD | metabat2 | 2.15 |
| METABAT2_METABAT2 | metabat2 | 2.17 |
| METABINNER_KMER | MetaBinner | 1.4.4-0 |
| python | 3.7.6 | |
| METABINNER_TOOSHORT | MetaBinner | 1.4.4-0 |
| python | 3.7.6 | |
| METASPADES | spades | 4.1.0 |
| PRODIGAL | pigz | 2.6 |
| prodigal | 2.6.3 | |
| QUAST | metaquast | 5.0.2 |
| python | 3.7.6 | |
| QUAST_BINS | metaquast | 5.0.2 |
| python | 3.7.6 | |
| QUAST_BINS_SUMMARY | cp | 9.5 |
| SEMIBIN_SINGLEEASYBIN | SemiBin | 2.2.0 |
| SEQKIT_STATS | seqkit | 2.9.0 |
| SPLIT_FASTA | biopython | 1.7.4 |
| pandas | 1.1.5 | |
| python | 3.6.7 | |
| Workflow | Nextflow | 25.10.3 |
| nf-core/mag | v5.5.0dev-ga6d77dd | |
| fastp | fastp | 1.0.1 |
nf-core/mag Methods Description
Suggested text and references to use when describing pipeline usage within the methods section of a publication.URL: https://github.com/nf-core/mag
Methods
Data was processed using nf-core/mag v5.5.0dev ((doi: 10.1093/nargab/lqac007); Krakau et al., 2022) of the nf-core collection of workflows (Ewels et al., 2020), utilising reproducible software environments from the Bioconda (Grüning et al., 2018) and Biocontainers (da Veiga Leprevost et al., 2017) projects.
The pipeline was executed with Nextflow v25.10.3 (Di Tommaso et al., 2017) with the following command:
nextflow run nf-core/mag -r minimap2-yaml-issue -profile apptainer -c /project2/ckenkel_26/liruiqi/Osedax_meta/CARC_mag_slurm.config --input /project2/ckenkel_26/liruiqi/Osedax_meta/CR180008_Osedax_frankpressi/CR180008_O_frankpressi_samplesheet.csv --outdir /project2/ckenkel_26/liruiqi/Osedax_meta/CR180008_Osedax_frankpressi --gtdb_db /project2/ckenkel_26/liruiqi/mag_out_project2/gtdb226/release226 --host_fasta /project2/ckenkel_26/liruiqi/Osedax_meta/Osedax_frankpressi.fna --host_removal_verysensitive --run_checkm2 --save_hostremoved_reads --skip_megahit --skip_prokka --save_assembly_mapped_reads -resumeReferences
- Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. doi: 10.1038/nbt.3820
- Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. doi: 10.1038/s41587-020-0439-x
- Krakau, S., Straub, D., Gourlé, H., Gabernet, G., & Nahnsen, S. (2022). nf-core/mag: a best-practice pipeline for metagenome hybrid assembly and binning. NAR Genomics and Bioinformatics, 4(1). https://doi.org/10.1038/s41587-020-0439-x
- Grüning, B., Dale, R., Sjödin, A., Chapman, B. A., Rowe, J., Tomkins-Tinch, C. H., Valieris, R., Köster, J., & Bioconda Team. (2018). Bioconda: sustainable and comprehensive software distribution for the life sciences. Nature Methods, 15(7), 475–476. doi: 10.1038/s41592-018-0046-7
- da Veiga Leprevost, F., Grüning, B. A., Alves Aflitos, S., Röst, H. L., Uszkoreit, J., Barsnes, H., Vaudel, M., Moreno, P., Gatto, L., Weber, J., Bai, M., Jimenez, R. C., Sachsenberg, T., Pfeuffer, J., Vera Alvarez, R., Griss, J., Nesvizhskii, A. I., & Perez-Riverol, Y. (2017). BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics (Oxford, England), 33(16), 2580–2582. doi: 10.1093/bioinformatics/btx192
Notes:
- The command above does not include parameters contained in any configs or profiles that may have been used. Ensure the config file is also uploaded with your publication!
- You should also cite all software used within this run. Check the "Software Versions" of this report to get version information.
nf-core/mag Workflow Summary
- this information is collected when the pipeline is started.URL: https://github.com/nf-core/mag
Input/output options
- input
- /project2/ckenkel_26/liruiqi/Osedax_meta/CR180008_Osedax_frankpressi/CR180008_O_frankpressi_samplesheet.csv
- outdir
- /project2/ckenkel_26/liruiqi/Osedax_meta/CR180008_Osedax_frankpressi
Generic options
- trace_report_suffix
- 2026-03-05_19-31-34
Quality control for short reads options
- host_fasta
- /project2/ckenkel_26/liruiqi/Osedax_meta/Osedax_frankpressi.fna
- host_removal_verysensitive
- true
- save_hostremoved_reads
- true
Taxonomic profiling options
- gtdb_db
- /project2/ckenkel_26/liruiqi/mag_out_project2/gtdb226/release226
- gtdbtk_max_contamination
- 10.0
- gtdbtk_min_completeness
- 50.0
Assembly options
- skip_megahit
- true
Gene prediction and annotation options
- skip_prokka
- true
Binning options
- save_assembly_mapped_reads
- true
Bin quality check options
- run_busco
- true
- run_checkm2
- true
Core Nextflow options
- configFiles
- /home1/liruiqi/.nextflow/assets/nf-core/mag/nextflow.config, /project2/ckenkel_26/liruiqi/Osedax_meta/CARC_mag_slurm.config
- containerEngine
- apptainer
- launchDir
- /project2/ckenkel_26/liruiqi/Osedax_meta/CR180008_Osedax_frankpressi
- profile
- apptainer
- projectDir
- /home1/liruiqi/.nextflow/assets/nf-core/mag
- revision
- minimap2-yaml-issue
- runName
- elated_meninsky
- userName
- liruiqi
- workDir
- /project2/ckenkel_26/liruiqi/Osedax_meta/CR180008_Osedax_frankpressi/work
