{ "input": "/scratch1/liruiqi/meta_Osedax/mag_outputs/samplesheet.csv", "assembly_input": null, "single_end": false, "skip_clipping": false, "clip_tool": "fastp", "save_clipped_reads": false, "reads_minlength": 15, "fastp_save_trimmed_fail": false, "fastp_qualified_quality": 15, "fastp_cut_mean_quality": 15, "fastp_trim_polyg": false, "adapterremoval_minquality": 2, "adapterremoval_adapter1": "AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG", "adapterremoval_adapter2": "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT", "adapterremoval_trim_quality_stretch": false, "keep_phix": false, "skip_shortread_qc": false, "longread_adaptertrimming_tool": "porechop_abi", "longread_filtering_tool": "filtlong", "phix_reference": null, "save_phixremoved_reads": false, "host_fasta": "/scratch1/liruiqi/meta_Osedax/sylph_outputs/osedax_db/Osedax_frankpressi.fna", "host_fasta_bowtie2index": null, "host_genome": null, "host_removal_verysensitive": true, "host_removal_save_ids": false, "save_hostremoved_reads": false, "bbnorm": false, "bbnorm_target": 100, "bbnorm_min": 5, "save_bbnorm_reads": false, "bowtie2_mode": null, "binning_map_mode": "group", "save_assembly_mapped_reads": false, "skip_binning": false, "min_contig_size": 1500, "min_length_unbinned_contigs": 1000000, "max_unbinned_contigs": 100, "skip_prokka": false, "longread_percentidentity": null, "shortread_percentidentity": null, "prokka_fast_mode": false, "prokka_with_compliance": false, "prokka_compliance_centre": null, "coassemble_group": false, "spades_options": null, "spades_downstreaminput": "scaffolds", "megahit_options": null, "skip_spades": false, "skip_spadeshybrid": false, "skip_megahit": false, "skip_ale": false, "skip_quast": false, "skip_prodigal": false, "skip_metamdbg": false, "skip_flye": false, "run_virus_identification": false, "genomad_db": null, "genomad_min_score": 0.7, "genomad_splits": 1, "ancient_dna": false, "pydamage_accuracy": 0.5, "skip_ancient_damagecorrection": false, "freebayes_ploidy": 1, "freebayes_min_basequality": 20, "freebayes_minallelefreq": 0.33, "bcftools_view_high_variant_quality": 30, "bcftools_view_medium_variant_quality": 20, "bcftools_view_minimal_allelesupport": 3, "cat_db": null, "cat_db_generate": false, "cat_allow_unofficial_lineages": false, "cat_classify_unbinned": false, "cat_no_suggestive_asterisks": false, "save_cat_db": false, "skip_gtdbtk": false, "gtdb_db": "https://data.gtdb.aau.ecogenomic.org/releases/release226/226.0/auxillary_files/gtdbtk_package/full_package/gtdbtk_r226_data.tar.gz", "gtdbtk_min_completeness": 50.0, "gtdbtk_max_contamination": 10.0, "gtdbtk_min_perc_aa": 10, "gtdbtk_min_af": 0.65, "gtdbtk_pplacer_cpus": 1, "gtdbtk_pplacer_useram": false, "gtdbtk_use_full_tree": false, "gtdbtk_skip_aniscreen": false, "skip_adapter_trimming": false, "skip_longread_filtering": false, "skip_longread_qc": false, "keep_lambda": false, "longreads_min_quality": null, "longreads_min_length": 1000, "longreads_keep_percent": 90, "longreads_length_weight": 10, "lambda_reference": null, "save_lambdaremoved_reads": false, "save_porechop_reads": false, "save_filtered_longreads": false, "skip_metabat2": false, "skip_maxbin2": false, "skip_metabinner": false, "bin_metabinner_scale": "large", "skip_concoct": false, "skip_comebin": false, "skip_semibin": false, "semibin_rng_seed": 1, "semibin_environment": "global", "bin_concoct_chunksize": 10000, "bin_concoct_overlap": 0, "bin_concoct_donotconcatlast": false, "bin_min_size": 0, "bin_max_size": null, "bin_domain_classification": false, "bin_domain_classification_tool": "tiara", "tiara_min_length": 3000, "refine_bins_dastool": false, "refine_bins_dastool_threshold": 0.5, "refine_bins_dastool_savecontig2bin": false, "postbinning_input": "raw_bins_only", "exclude_unbins_from_postbinning": false, "skip_binqc": false, "run_busco": true, "run_checkm": false, "run_checkm2": false, "busco_db": null, "busco_db_lineage": "auto", "save_busco_db": false, "busco_clean": false, "checkm_download_url": "https://zenodo.org/records/7401545/files/checkm_data_2015_01_16.tar.gz", "checkm_db": null, "save_checkm_data": false, "checkm2_db": null, "checkm2_db_version": 14897628, "save_checkm2_data": false, "run_gunc": false, "gunc_database_type": "progenomes", "gunc_db": null, "gunc_save_db": false, "generate_bigmag_file": false, "megahit_fix_cpu_1": false, "spades_fix_cpus": 16, "spadeshybrid_fix_cpus": -1, "metabat_rng_seed": 1, "skip_metaeuk": false, "metaeuk_mmseqs_db": null, "metaeuk_db": null, "save_mmseqs_db": false, "igenomes_base": "s3://ngi-igenomes/igenomes/", "igenomes_ignore": false, "multiqc_config": null, "multiqc_title": null, "multiqc_logo": null, "max_multiqc_email_size": "25.MB", "multiqc_methods_description": null, "outdir": "/scratch1/liruiqi/meta_Osedax/mag_outputs", "publish_dir_mode": "copy", "email": null, "email_on_fail": null, "plaintext_email": false, "monochrome_logs": false, "hook_url": null, "help": false, "help_full": false, "show_hidden": false, "version": false, "pipelines_testdata_base_path": "https://raw.githubusercontent.com/nf-core/test-datasets/", "trace_report_suffix": "2026-02-07_17-41-30", "config_profile_name": null, "config_profile_description": null, "custom_config_version": "master", "custom_config_base": "https://raw.githubusercontent.com/nf-core/configs/master", "config_profile_contact": null, "config_profile_url": null, "validate_params": true, "genomes": { "GRCh37": { "fasta": "s3://ngi-igenomes/igenomes//Homo_sapiens/Ensembl/GRCh37/Sequence/WholeGenomeFasta/genome.fa", "bwa": "s3://ngi-igenomes/igenomes//Homo_sapiens/Ensembl/GRCh37/Sequence/BWAIndex/version0.6.0/", "bowtie2": "s3://ngi-igenomes/igenomes//Homo_sapiens/Ensembl/GRCh37/Sequence/Bowtie2Index/", "star": "s3://ngi-igenomes/igenomes//Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/", "bismark": "s3://ngi-igenomes/igenomes//Homo_sapiens/Ensembl/GRCh37/Sequence/BismarkIndex/", "gtf": "s3://ngi-igenomes/igenomes//Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf", "bed12": "s3://ngi-igenomes/igenomes//Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.bed", "readme": "s3://ngi-igenomes/igenomes//Homo_sapiens/Ensembl/GRCh37/Annotation/README.txt", "mito_name": "MT", "macs_gsize": "2.7e9", "blacklist": "/home1/liruiqi/.nextflow/assets/nf-core/mag/assets/blacklists/GRCh37-blacklist.bed" }, "GRCh38": { "fasta": "s3://ngi-igenomes/igenomes//Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa", "bwa": "s3://ngi-igenomes/igenomes//Homo_sapiens/NCBI/GRCh38/Sequence/BWAIndex/version0.6.0/", "bowtie2": "s3://ngi-igenomes/igenomes//Homo_sapiens/NCBI/GRCh38/Sequence/Bowtie2Index/", "star": "s3://ngi-igenomes/igenomes//Homo_sapiens/NCBI/GRCh38/Sequence/STARIndex/", "bismark": "s3://ngi-igenomes/igenomes//Homo_sapiens/NCBI/GRCh38/Sequence/BismarkIndex/", "gtf": "s3://ngi-igenomes/igenomes//Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.gtf", "bed12": "s3://ngi-igenomes/igenomes//Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.bed", "mito_name": "chrM", "macs_gsize": "2.7e9", "blacklist": "/home1/liruiqi/.nextflow/assets/nf-core/mag/assets/blacklists/hg38-blacklist.bed" }, "CHM13": { "fasta": "s3://ngi-igenomes/igenomes//Homo_sapiens/UCSC/CHM13/Sequence/WholeGenomeFasta/genome.fa", "bwa": "s3://ngi-igenomes/igenomes//Homo_sapiens/UCSC/CHM13/Sequence/BWAIndex/", "bwamem2": "s3://ngi-igenomes/igenomes//Homo_sapiens/UCSC/CHM13/Sequence/BWAmem2Index/", "gtf": "s3://ngi-igenomes/igenomes//Homo_sapiens/NCBI/CHM13/Annotation/Genes/genes.gtf", "gff": "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/914/755/GCF_009914755.1_T2T-CHM13v2.0/GCF_009914755.1_T2T-CHM13v2.0_genomic.gff.gz", "mito_name": "chrM" }, "GRCm38": { "fasta": "s3://ngi-igenomes/igenomes//Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa", "bwa": "s3://ngi-igenomes/igenomes//Mus_musculus/Ensembl/GRCm38/Sequence/BWAIndex/version0.6.0/", "bowtie2": "s3://ngi-igenomes/igenomes//Mus_musculus/Ensembl/GRCm38/Sequence/Bowtie2Index/", "star": "s3://ngi-igenomes/igenomes//Mus_musculus/Ensembl/GRCm38/Sequence/STARIndex/", "bismark": "s3://ngi-igenomes/igenomes//Mus_musculus/Ensembl/GRCm38/Sequence/BismarkIndex/", "gtf": "s3://ngi-igenomes/igenomes//Mus_musculus/Ensembl/GRCm38/Annotation/Genes/genes.gtf", "bed12": "s3://ngi-igenomes/igenomes//Mus_musculus/Ensembl/GRCm38/Annotation/Genes/genes.bed", "readme": "s3://ngi-igenomes/igenomes//Mus_musculus/Ensembl/GRCm38/Annotation/README.txt", "mito_name": "MT", "macs_gsize": "1.87e9", "blacklist": "/home1/liruiqi/.nextflow/assets/nf-core/mag/assets/blacklists/GRCm38-blacklist.bed" }, "TAIR10": { "fasta": "s3://ngi-igenomes/igenomes//Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/WholeGenomeFasta/genome.fa", "bwa": "s3://ngi-igenomes/igenomes//Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BWAIndex/version0.6.0/", "bowtie2": "s3://ngi-igenomes/igenomes//Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/Bowtie2Index/", "star": "s3://ngi-igenomes/igenomes//Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/STARIndex/", "bismark": "s3://ngi-igenomes/igenomes//Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BismarkIndex/", "gtf": "s3://ngi-igenomes/igenomes//Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/Genes/genes.gtf", "bed12": "s3://ngi-igenomes/igenomes//Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/Genes/genes.bed", "readme": "s3://ngi-igenomes/igenomes//Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/README.txt", "mito_name": "Mt" }, "EB2": { "fasta": "s3://ngi-igenomes/igenomes//Bacillus_subtilis_168/Ensembl/EB2/Sequence/WholeGenomeFasta/genome.fa", "bwa": "s3://ngi-igenomes/igenomes//Bacillus_subtilis_168/Ensembl/EB2/Sequence/BWAIndex/version0.6.0/", "bowtie2": "s3://ngi-igenomes/igenomes//Bacillus_subtilis_168/Ensembl/EB2/Sequence/Bowtie2Index/", "star": "s3://ngi-igenomes/igenomes//Bacillus_subtilis_168/Ensembl/EB2/Sequence/STARIndex/", "bismark": "s3://ngi-igenomes/igenomes//Bacillus_subtilis_168/Ensembl/EB2/Sequence/BismarkIndex/", "gtf": "s3://ngi-igenomes/igenomes//Bacillus_subtilis_168/Ensembl/EB2/Annotation/Genes/genes.gtf", "bed12": "s3://ngi-igenomes/igenomes//Bacillus_subtilis_168/Ensembl/EB2/Annotation/Genes/genes.bed", "readme": "s3://ngi-igenomes/igenomes//Bacillus_subtilis_168/Ensembl/EB2/Annotation/README.txt" }, "UMD3.1": { "fasta": "s3://ngi-igenomes/igenomes//Bos_taurus/Ensembl/UMD3.1/Sequence/WholeGenomeFasta/genome.fa", "bwa": "s3://ngi-igenomes/igenomes//Bos_taurus/Ensembl/UMD3.1/Sequence/BWAIndex/version0.6.0/", "bowtie2": "s3://ngi-igenomes/igenomes//Bos_taurus/Ensembl/UMD3.1/Sequence/Bowtie2Index/", "star": "s3://ngi-igenomes/igenomes//Bos_taurus/Ensembl/UMD3.1/Sequence/STARIndex/", "bismark": "s3://ngi-igenomes/igenomes//Bos_taurus/Ensembl/UMD3.1/Sequence/BismarkIndex/", "gtf": "s3://ngi-igenomes/igenomes//Bos_taurus/Ensembl/UMD3.1/Annotation/Genes/genes.gtf", "bed12": "s3://ngi-igenomes/igenomes//Bos_taurus/Ensembl/UMD3.1/Annotation/Genes/genes.bed", "readme": "s3://ngi-igenomes/igenomes//Bos_taurus/Ensembl/UMD3.1/Annotation/README.txt", "mito_name": "MT" }, "WBcel235": { "fasta": "s3://ngi-igenomes/igenomes//Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/WholeGenomeFasta/genome.fa", "bwa": "s3://ngi-igenomes/igenomes//Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BWAIndex/version0.6.0/", "bowtie2": "s3://ngi-igenomes/igenomes//Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/Bowtie2Index/", "star": "s3://ngi-igenomes/igenomes//Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/STARIndex/", "bismark": "s3://ngi-igenomes/igenomes//Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BismarkIndex/", "gtf": "s3://ngi-igenomes/igenomes//Caenorhabditis_elegans/Ensembl/WBcel235/Annotation/Genes/genes.gtf", "bed12": "s3://ngi-igenomes/igenomes//Caenorhabditis_elegans/Ensembl/WBcel235/Annotation/Genes/genes.bed", "mito_name": "MtDNA", "macs_gsize": "9e7" }, "CanFam3.1": { "fasta": "s3://ngi-igenomes/igenomes//Canis_familiaris/Ensembl/CanFam3.1/Sequence/WholeGenomeFasta/genome.fa", "bwa": "s3://ngi-igenomes/igenomes//Canis_familiaris/Ensembl/CanFam3.1/Sequence/BWAIndex/version0.6.0/", "bowtie2": "s3://ngi-igenomes/igenomes//Canis_familiaris/Ensembl/CanFam3.1/Sequence/Bowtie2Index/", "star": "s3://ngi-igenomes/igenomes//Canis_familiaris/Ensembl/CanFam3.1/Sequence/STARIndex/", "bismark": "s3://ngi-igenomes/igenomes//Canis_familiaris/Ensembl/CanFam3.1/Sequence/BismarkIndex/", "gtf": "s3://ngi-igenomes/igenomes//Canis_familiaris/Ensembl/CanFam3.1/Annotation/Genes/genes.gtf", "bed12": "s3://ngi-igenomes/igenomes//Canis_familiaris/Ensembl/CanFam3.1/Annotation/Genes/genes.bed", "readme": "s3://ngi-igenomes/igenomes//Canis_familiaris/Ensembl/CanFam3.1/Annotation/README.txt", "mito_name": "MT" }, "GRCz10": { "fasta": "s3://ngi-igenomes/igenomes//Danio_rerio/Ensembl/GRCz10/Sequence/WholeGenomeFasta/genome.fa", "bwa": "s3://ngi-igenomes/igenomes//Danio_rerio/Ensembl/GRCz10/Sequence/BWAIndex/version0.6.0/", "bowtie2": "s3://ngi-igenomes/igenomes//Danio_rerio/Ensembl/GRCz10/Sequence/Bowtie2Index/", "star": "s3://ngi-igenomes/igenomes//Danio_rerio/Ensembl/GRCz10/Sequence/STARIndex/", "bismark": "s3://ngi-igenomes/igenomes//Danio_rerio/Ensembl/GRCz10/Sequence/BismarkIndex/", "gtf": "s3://ngi-igenomes/igenomes//Danio_rerio/Ensembl/GRCz10/Annotation/Genes/genes.gtf", "bed12": "s3://ngi-igenomes/igenomes//Danio_rerio/Ensembl/GRCz10/Annotation/Genes/genes.bed", "mito_name": "MT" }, "BDGP6": { "fasta": "s3://ngi-igenomes/igenomes//Drosophila_melanogaster/Ensembl/BDGP6/Sequence/WholeGenomeFasta/genome.fa", "bwa": "s3://ngi-igenomes/igenomes//Drosophila_melanogaster/Ensembl/BDGP6/Sequence/BWAIndex/version0.6.0/", "bowtie2": "s3://ngi-igenomes/igenomes//Drosophila_melanogaster/Ensembl/BDGP6/Sequence/Bowtie2Index/", "star": "s3://ngi-igenomes/igenomes//Drosophila_melanogaster/Ensembl/BDGP6/Sequence/STARIndex/", "bismark": "s3://ngi-igenomes/igenomes//Drosophila_melanogaster/Ensembl/BDGP6/Sequence/BismarkIndex/", "gtf": "s3://ngi-igenomes/igenomes//Drosophila_melanogaster/Ensembl/BDGP6/Annotation/Genes/genes.gtf", "bed12": "s3://ngi-igenomes/igenomes//Drosophila_melanogaster/Ensembl/BDGP6/Annotation/Genes/genes.bed", "mito_name": "M", "macs_gsize": "1.2e8" }, "EquCab2": { "fasta": "s3://ngi-igenomes/igenomes//Equus_caballus/Ensembl/EquCab2/Sequence/WholeGenomeFasta/genome.fa", "bwa": "s3://ngi-igenomes/igenomes//Equus_caballus/Ensembl/EquCab2/Sequence/BWAIndex/version0.6.0/", "bowtie2": "s3://ngi-igenomes/igenomes//Equus_caballus/Ensembl/EquCab2/Sequence/Bowtie2Index/", "star": "s3://ngi-igenomes/igenomes//Equus_caballus/Ensembl/EquCab2/Sequence/STARIndex/", "bismark": "s3://ngi-igenomes/igenomes//Equus_caballus/Ensembl/EquCab2/Sequence/BismarkIndex/", "gtf": "s3://ngi-igenomes/igenomes//Equus_caballus/Ensembl/EquCab2/Annotation/Genes/genes.gtf", "bed12": "s3://ngi-igenomes/igenomes//Equus_caballus/Ensembl/EquCab2/Annotation/Genes/genes.bed", "readme": "s3://ngi-igenomes/igenomes//Equus_caballus/Ensembl/EquCab2/Annotation/README.txt", "mito_name": "MT" }, "EB1": { "fasta": "s3://ngi-igenomes/igenomes//Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/WholeGenomeFasta/genome.fa", "bwa": "s3://ngi-igenomes/igenomes//Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/BWAIndex/version0.6.0/", "bowtie2": "s3://ngi-igenomes/igenomes//Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/Bowtie2Index/", "star": "s3://ngi-igenomes/igenomes//Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/STARIndex/", "bismark": "s3://ngi-igenomes/igenomes//Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/BismarkIndex/", "gtf": "s3://ngi-igenomes/igenomes//Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/Genes/genes.gtf", "bed12": "s3://ngi-igenomes/igenomes//Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/Genes/genes.bed", "readme": "s3://ngi-igenomes/igenomes//Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/README.txt" }, "Galgal4": { "fasta": "s3://ngi-igenomes/igenomes//Gallus_gallus/Ensembl/Galgal4/Sequence/WholeGenomeFasta/genome.fa", "bwa": "s3://ngi-igenomes/igenomes//Gallus_gallus/Ensembl/Galgal4/Sequence/BWAIndex/version0.6.0/", "bowtie2": "s3://ngi-igenomes/igenomes//Gallus_gallus/Ensembl/Galgal4/Sequence/Bowtie2Index/", "star": "s3://ngi-igenomes/igenomes//Gallus_gallus/Ensembl/Galgal4/Sequence/STARIndex/", "bismark": "s3://ngi-igenomes/igenomes//Gallus_gallus/Ensembl/Galgal4/Sequence/BismarkIndex/", "gtf": "s3://ngi-igenomes/igenomes//Gallus_gallus/Ensembl/Galgal4/Annotation/Genes/genes.gtf", "bed12": "s3://ngi-igenomes/igenomes//Gallus_gallus/Ensembl/Galgal4/Annotation/Genes/genes.bed", "mito_name": "MT" }, "Gm01": { "fasta": "s3://ngi-igenomes/igenomes//Glycine_max/Ensembl/Gm01/Sequence/WholeGenomeFasta/genome.fa", "bwa": "s3://ngi-igenomes/igenomes//Glycine_max/Ensembl/Gm01/Sequence/BWAIndex/version0.6.0/", "bowtie2": "s3://ngi-igenomes/igenomes//Glycine_max/Ensembl/Gm01/Sequence/Bowtie2Index/", "star": "s3://ngi-igenomes/igenomes//Glycine_max/Ensembl/Gm01/Sequence/STARIndex/", "bismark": "s3://ngi-igenomes/igenomes//Glycine_max/Ensembl/Gm01/Sequence/BismarkIndex/", "gtf": "s3://ngi-igenomes/igenomes//Glycine_max/Ensembl/Gm01/Annotation/Genes/genes.gtf", "bed12": "s3://ngi-igenomes/igenomes//Glycine_max/Ensembl/Gm01/Annotation/Genes/genes.bed", "readme": "s3://ngi-igenomes/igenomes//Glycine_max/Ensembl/Gm01/Annotation/README.txt" }, "Mmul_1": { "fasta": "s3://ngi-igenomes/igenomes//Macaca_mulatta/Ensembl/Mmul_1/Sequence/WholeGenomeFasta/genome.fa", "bwa": "s3://ngi-igenomes/igenomes//Macaca_mulatta/Ensembl/Mmul_1/Sequence/BWAIndex/version0.6.0/", "bowtie2": "s3://ngi-igenomes/igenomes//Macaca_mulatta/Ensembl/Mmul_1/Sequence/Bowtie2Index/", "star": "s3://ngi-igenomes/igenomes//Macaca_mulatta/Ensembl/Mmul_1/Sequence/STARIndex/", "bismark": "s3://ngi-igenomes/igenomes//Macaca_mulatta/Ensembl/Mmul_1/Sequence/BismarkIndex/", "gtf": "s3://ngi-igenomes/igenomes//Macaca_mulatta/Ensembl/Mmul_1/Annotation/Genes/genes.gtf", "bed12": "s3://ngi-igenomes/igenomes//Macaca_mulatta/Ensembl/Mmul_1/Annotation/Genes/genes.bed", "readme": "s3://ngi-igenomes/igenomes//Macaca_mulatta/Ensembl/Mmul_1/Annotation/README.txt", "mito_name": "MT" }, "IRGSP-1.0": { "fasta": "s3://ngi-igenomes/igenomes//Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/WholeGenomeFasta/genome.fa", "bwa": "s3://ngi-igenomes/igenomes//Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/BWAIndex/version0.6.0/", "bowtie2": "s3://ngi-igenomes/igenomes//Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/Bowtie2Index/", "star": "s3://ngi-igenomes/igenomes//Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/STARIndex/", "bismark": "s3://ngi-igenomes/igenomes//Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/BismarkIndex/", "gtf": "s3://ngi-igenomes/igenomes//Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Annotation/Genes/genes.gtf", "bed12": "s3://ngi-igenomes/igenomes//Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Annotation/Genes/genes.bed", "mito_name": "Mt" }, "CHIMP2.1.4": { "fasta": "s3://ngi-igenomes/igenomes//Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/WholeGenomeFasta/genome.fa", "bwa": "s3://ngi-igenomes/igenomes//Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/BWAIndex/version0.6.0/", "bowtie2": "s3://ngi-igenomes/igenomes//Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/Bowtie2Index/", "star": "s3://ngi-igenomes/igenomes//Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/STARIndex/", "bismark": "s3://ngi-igenomes/igenomes//Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/BismarkIndex/", "gtf": "s3://ngi-igenomes/igenomes//Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/Genes/genes.gtf", "bed12": "s3://ngi-igenomes/igenomes//Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/Genes/genes.bed", "readme": "s3://ngi-igenomes/igenomes//Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/README.txt", "mito_name": "MT" }, "Rnor_5.0": { "fasta": "s3://ngi-igenomes/igenomes//Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/WholeGenomeFasta/genome.fa", "bwa": "s3://ngi-igenomes/igenomes//Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/BWAIndex/version0.6.0/", "bowtie2": "s3://ngi-igenomes/igenomes//Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/Bowtie2Index/", "star": "s3://ngi-igenomes/igenomes//Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/STARIndex/", "bismark": "s3://ngi-igenomes/igenomes//Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/BismarkIndex/", "gtf": "s3://ngi-igenomes/igenomes//Rattus_norvegicus/Ensembl/Rnor_5.0/Annotation/Genes/genes.gtf", "bed12": "s3://ngi-igenomes/igenomes//Rattus_norvegicus/Ensembl/Rnor_5.0/Annotation/Genes/genes.bed", "mito_name": "MT" }, "Rnor_6.0": { "fasta": "s3://ngi-igenomes/igenomes//Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/WholeGenomeFasta/genome.fa", "bwa": "s3://ngi-igenomes/igenomes//Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/BWAIndex/version0.6.0/", "bowtie2": "s3://ngi-igenomes/igenomes//Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/Bowtie2Index/", "star": "s3://ngi-igenomes/igenomes//Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/STARIndex/", "bismark": "s3://ngi-igenomes/igenomes//Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/BismarkIndex/", "gtf": "s3://ngi-igenomes/igenomes//Rattus_norvegicus/Ensembl/Rnor_6.0/Annotation/Genes/genes.gtf", "bed12": "s3://ngi-igenomes/igenomes//Rattus_norvegicus/Ensembl/Rnor_6.0/Annotation/Genes/genes.bed", "mito_name": "MT" }, "R64-1-1": { "fasta": "s3://ngi-igenomes/igenomes//Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/WholeGenomeFasta/genome.fa", "bwa": "s3://ngi-igenomes/igenomes//Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BWAIndex/version0.6.0/", "bowtie2": "s3://ngi-igenomes/igenomes//Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/Bowtie2Index/", "star": "s3://ngi-igenomes/igenomes//Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/STARIndex/", "bismark": "s3://ngi-igenomes/igenomes//Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BismarkIndex/", "gtf": "s3://ngi-igenomes/igenomes//Saccharomyces_cerevisiae/Ensembl/R64-1-1/Annotation/Genes/genes.gtf", "bed12": "s3://ngi-igenomes/igenomes//Saccharomyces_cerevisiae/Ensembl/R64-1-1/Annotation/Genes/genes.bed", "mito_name": "MT", "macs_gsize": "1.2e7" }, "EF2": { "fasta": "s3://ngi-igenomes/igenomes//Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/WholeGenomeFasta/genome.fa", "bwa": "s3://ngi-igenomes/igenomes//Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BWAIndex/version0.6.0/", "bowtie2": "s3://ngi-igenomes/igenomes//Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/Bowtie2Index/", "star": "s3://ngi-igenomes/igenomes//Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/STARIndex/", "bismark": "s3://ngi-igenomes/igenomes//Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BismarkIndex/", "gtf": "s3://ngi-igenomes/igenomes//Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/Genes/genes.gtf", "bed12": "s3://ngi-igenomes/igenomes//Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/Genes/genes.bed", "readme": "s3://ngi-igenomes/igenomes//Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/README.txt", "mito_name": "MT", "macs_gsize": "1.21e7" }, "Sbi1": { "fasta": "s3://ngi-igenomes/igenomes//Sorghum_bicolor/Ensembl/Sbi1/Sequence/WholeGenomeFasta/genome.fa", "bwa": "s3://ngi-igenomes/igenomes//Sorghum_bicolor/Ensembl/Sbi1/Sequence/BWAIndex/version0.6.0/", "bowtie2": "s3://ngi-igenomes/igenomes//Sorghum_bicolor/Ensembl/Sbi1/Sequence/Bowtie2Index/", "star": "s3://ngi-igenomes/igenomes//Sorghum_bicolor/Ensembl/Sbi1/Sequence/STARIndex/", "bismark": "s3://ngi-igenomes/igenomes//Sorghum_bicolor/Ensembl/Sbi1/Sequence/BismarkIndex/", "gtf": "s3://ngi-igenomes/igenomes//Sorghum_bicolor/Ensembl/Sbi1/Annotation/Genes/genes.gtf", "bed12": "s3://ngi-igenomes/igenomes//Sorghum_bicolor/Ensembl/Sbi1/Annotation/Genes/genes.bed", "readme": "s3://ngi-igenomes/igenomes//Sorghum_bicolor/Ensembl/Sbi1/Annotation/README.txt" }, "Sscrofa10.2": { "fasta": "s3://ngi-igenomes/igenomes//Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/WholeGenomeFasta/genome.fa", "bwa": "s3://ngi-igenomes/igenomes//Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/BWAIndex/version0.6.0/", "bowtie2": "s3://ngi-igenomes/igenomes//Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/Bowtie2Index/", "star": "s3://ngi-igenomes/igenomes//Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/STARIndex/", "bismark": "s3://ngi-igenomes/igenomes//Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/BismarkIndex/", "gtf": "s3://ngi-igenomes/igenomes//Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/Genes/genes.gtf", "bed12": "s3://ngi-igenomes/igenomes//Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/Genes/genes.bed", "readme": "s3://ngi-igenomes/igenomes//Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/README.txt", "mito_name": "MT" }, "AGPv3": { "fasta": "s3://ngi-igenomes/igenomes//Zea_mays/Ensembl/AGPv3/Sequence/WholeGenomeFasta/genome.fa", "bwa": "s3://ngi-igenomes/igenomes//Zea_mays/Ensembl/AGPv3/Sequence/BWAIndex/version0.6.0/", "bowtie2": "s3://ngi-igenomes/igenomes//Zea_mays/Ensembl/AGPv3/Sequence/Bowtie2Index/", "star": "s3://ngi-igenomes/igenomes//Zea_mays/Ensembl/AGPv3/Sequence/STARIndex/", "bismark": "s3://ngi-igenomes/igenomes//Zea_mays/Ensembl/AGPv3/Sequence/BismarkIndex/", "gtf": "s3://ngi-igenomes/igenomes//Zea_mays/Ensembl/AGPv3/Annotation/Genes/genes.gtf", "bed12": "s3://ngi-igenomes/igenomes//Zea_mays/Ensembl/AGPv3/Annotation/Genes/genes.bed", "mito_name": "Mt" }, "hg38": { "fasta": "s3://ngi-igenomes/igenomes//Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.fa", "bwa": "s3://ngi-igenomes/igenomes//Homo_sapiens/UCSC/hg38/Sequence/BWAIndex/version0.6.0/", "bowtie2": "s3://ngi-igenomes/igenomes//Homo_sapiens/UCSC/hg38/Sequence/Bowtie2Index/", "star": "s3://ngi-igenomes/igenomes//Homo_sapiens/UCSC/hg38/Sequence/STARIndex/", "bismark": "s3://ngi-igenomes/igenomes//Homo_sapiens/UCSC/hg38/Sequence/BismarkIndex/", "gtf": "s3://ngi-igenomes/igenomes//Homo_sapiens/UCSC/hg38/Annotation/Genes/genes.gtf", "bed12": "s3://ngi-igenomes/igenomes//Homo_sapiens/UCSC/hg38/Annotation/Genes/genes.bed", "mito_name": "chrM", "macs_gsize": "2.7e9", "blacklist": "/home1/liruiqi/.nextflow/assets/nf-core/mag/assets/blacklists/hg38-blacklist.bed" }, "hg19": { "fasta": "s3://ngi-igenomes/igenomes//Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa", "bwa": "s3://ngi-igenomes/igenomes//Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/version0.6.0/", "bowtie2": "s3://ngi-igenomes/igenomes//Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/", "star": "s3://ngi-igenomes/igenomes//Homo_sapiens/UCSC/hg19/Sequence/STARIndex/", "bismark": "s3://ngi-igenomes/igenomes//Homo_sapiens/UCSC/hg19/Sequence/BismarkIndex/", "gtf": "s3://ngi-igenomes/igenomes//Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf", "bed12": "s3://ngi-igenomes/igenomes//Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.bed", "readme": "s3://ngi-igenomes/igenomes//Homo_sapiens/UCSC/hg19/Annotation/README.txt", "mito_name": "chrM", "macs_gsize": "2.7e9", "blacklist": "/home1/liruiqi/.nextflow/assets/nf-core/mag/assets/blacklists/hg19-blacklist.bed" }, "mm10": { "fasta": "s3://ngi-igenomes/igenomes//Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa", "bwa": "s3://ngi-igenomes/igenomes//Mus_musculus/UCSC/mm10/Sequence/BWAIndex/version0.6.0/", "bowtie2": "s3://ngi-igenomes/igenomes//Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/", "star": "s3://ngi-igenomes/igenomes//Mus_musculus/UCSC/mm10/Sequence/STARIndex/", "bismark": "s3://ngi-igenomes/igenomes//Mus_musculus/UCSC/mm10/Sequence/BismarkIndex/", "gtf": "s3://ngi-igenomes/igenomes//Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf", "bed12": "s3://ngi-igenomes/igenomes//Mus_musculus/UCSC/mm10/Annotation/Genes/genes.bed", "readme": "s3://ngi-igenomes/igenomes//Mus_musculus/UCSC/mm10/Annotation/README.txt", "mito_name": "chrM", "macs_gsize": "1.87e9", "blacklist": "/home1/liruiqi/.nextflow/assets/nf-core/mag/assets/blacklists/mm10-blacklist.bed" }, "bosTau8": { "fasta": "s3://ngi-igenomes/igenomes//Bos_taurus/UCSC/bosTau8/Sequence/WholeGenomeFasta/genome.fa", "bwa": "s3://ngi-igenomes/igenomes//Bos_taurus/UCSC/bosTau8/Sequence/BWAIndex/version0.6.0/", "bowtie2": "s3://ngi-igenomes/igenomes//Bos_taurus/UCSC/bosTau8/Sequence/Bowtie2Index/", "star": "s3://ngi-igenomes/igenomes//Bos_taurus/UCSC/bosTau8/Sequence/STARIndex/", "bismark": "s3://ngi-igenomes/igenomes//Bos_taurus/UCSC/bosTau8/Sequence/BismarkIndex/", "gtf": "s3://ngi-igenomes/igenomes//Bos_taurus/UCSC/bosTau8/Annotation/Genes/genes.gtf", "bed12": "s3://ngi-igenomes/igenomes//Bos_taurus/UCSC/bosTau8/Annotation/Genes/genes.bed", "mito_name": "chrM" }, "ce10": { "fasta": "s3://ngi-igenomes/igenomes//Caenorhabditis_elegans/UCSC/ce10/Sequence/WholeGenomeFasta/genome.fa", "bwa": "s3://ngi-igenomes/igenomes//Caenorhabditis_elegans/UCSC/ce10/Sequence/BWAIndex/version0.6.0/", "bowtie2": "s3://ngi-igenomes/igenomes//Caenorhabditis_elegans/UCSC/ce10/Sequence/Bowtie2Index/", "star": "s3://ngi-igenomes/igenomes//Caenorhabditis_elegans/UCSC/ce10/Sequence/STARIndex/", "bismark": "s3://ngi-igenomes/igenomes//Caenorhabditis_elegans/UCSC/ce10/Sequence/BismarkIndex/", "gtf": "s3://ngi-igenomes/igenomes//Caenorhabditis_elegans/UCSC/ce10/Annotation/Genes/genes.gtf", "bed12": "s3://ngi-igenomes/igenomes//Caenorhabditis_elegans/UCSC/ce10/Annotation/Genes/genes.bed", "readme": "s3://ngi-igenomes/igenomes//Caenorhabditis_elegans/UCSC/ce10/Annotation/README.txt", "mito_name": "chrM", "macs_gsize": "9e7" }, "canFam3": { "fasta": "s3://ngi-igenomes/igenomes//Canis_familiaris/UCSC/canFam3/Sequence/WholeGenomeFasta/genome.fa", "bwa": "s3://ngi-igenomes/igenomes//Canis_familiaris/UCSC/canFam3/Sequence/BWAIndex/version0.6.0/", "bowtie2": "s3://ngi-igenomes/igenomes//Canis_familiaris/UCSC/canFam3/Sequence/Bowtie2Index/", "star": "s3://ngi-igenomes/igenomes//Canis_familiaris/UCSC/canFam3/Sequence/STARIndex/", "bismark": "s3://ngi-igenomes/igenomes//Canis_familiaris/UCSC/canFam3/Sequence/BismarkIndex/", "gtf": "s3://ngi-igenomes/igenomes//Canis_familiaris/UCSC/canFam3/Annotation/Genes/genes.gtf", "bed12": "s3://ngi-igenomes/igenomes//Canis_familiaris/UCSC/canFam3/Annotation/Genes/genes.bed", "readme": "s3://ngi-igenomes/igenomes//Canis_familiaris/UCSC/canFam3/Annotation/README.txt", "mito_name": "chrM" }, "danRer10": { "fasta": "s3://ngi-igenomes/igenomes//Danio_rerio/UCSC/danRer10/Sequence/WholeGenomeFasta/genome.fa", "bwa": "s3://ngi-igenomes/igenomes//Danio_rerio/UCSC/danRer10/Sequence/BWAIndex/version0.6.0/", "bowtie2": "s3://ngi-igenomes/igenomes//Danio_rerio/UCSC/danRer10/Sequence/Bowtie2Index/", "star": "s3://ngi-igenomes/igenomes//Danio_rerio/UCSC/danRer10/Sequence/STARIndex/", "bismark": "s3://ngi-igenomes/igenomes//Danio_rerio/UCSC/danRer10/Sequence/BismarkIndex/", "gtf": "s3://ngi-igenomes/igenomes//Danio_rerio/UCSC/danRer10/Annotation/Genes/genes.gtf", "bed12": "s3://ngi-igenomes/igenomes//Danio_rerio/UCSC/danRer10/Annotation/Genes/genes.bed", "mito_name": "chrM", "macs_gsize": "1.37e9" }, "dm6": { "fasta": "s3://ngi-igenomes/igenomes//Drosophila_melanogaster/UCSC/dm6/Sequence/WholeGenomeFasta/genome.fa", "bwa": "s3://ngi-igenomes/igenomes//Drosophila_melanogaster/UCSC/dm6/Sequence/BWAIndex/version0.6.0/", "bowtie2": "s3://ngi-igenomes/igenomes//Drosophila_melanogaster/UCSC/dm6/Sequence/Bowtie2Index/", "star": "s3://ngi-igenomes/igenomes//Drosophila_melanogaster/UCSC/dm6/Sequence/STARIndex/", "bismark": "s3://ngi-igenomes/igenomes//Drosophila_melanogaster/UCSC/dm6/Sequence/BismarkIndex/", "gtf": "s3://ngi-igenomes/igenomes//Drosophila_melanogaster/UCSC/dm6/Annotation/Genes/genes.gtf", "bed12": "s3://ngi-igenomes/igenomes//Drosophila_melanogaster/UCSC/dm6/Annotation/Genes/genes.bed", "mito_name": "chrM", "macs_gsize": "1.2e8" }, "equCab2": { "fasta": "s3://ngi-igenomes/igenomes//Equus_caballus/UCSC/equCab2/Sequence/WholeGenomeFasta/genome.fa", "bwa": "s3://ngi-igenomes/igenomes//Equus_caballus/UCSC/equCab2/Sequence/BWAIndex/version0.6.0/", "bowtie2": "s3://ngi-igenomes/igenomes//Equus_caballus/UCSC/equCab2/Sequence/Bowtie2Index/", "star": "s3://ngi-igenomes/igenomes//Equus_caballus/UCSC/equCab2/Sequence/STARIndex/", "bismark": "s3://ngi-igenomes/igenomes//Equus_caballus/UCSC/equCab2/Sequence/BismarkIndex/", "gtf": "s3://ngi-igenomes/igenomes//Equus_caballus/UCSC/equCab2/Annotation/Genes/genes.gtf", "bed12": "s3://ngi-igenomes/igenomes//Equus_caballus/UCSC/equCab2/Annotation/Genes/genes.bed", "readme": "s3://ngi-igenomes/igenomes//Equus_caballus/UCSC/equCab2/Annotation/README.txt", "mito_name": "chrM" }, "galGal4": { "fasta": "s3://ngi-igenomes/igenomes//Gallus_gallus/UCSC/galGal4/Sequence/WholeGenomeFasta/genome.fa", "bwa": "s3://ngi-igenomes/igenomes//Gallus_gallus/UCSC/galGal4/Sequence/BWAIndex/version0.6.0/", "bowtie2": "s3://ngi-igenomes/igenomes//Gallus_gallus/UCSC/galGal4/Sequence/Bowtie2Index/", "star": "s3://ngi-igenomes/igenomes//Gallus_gallus/UCSC/galGal4/Sequence/STARIndex/", "bismark": "s3://ngi-igenomes/igenomes//Gallus_gallus/UCSC/galGal4/Sequence/BismarkIndex/", "gtf": "s3://ngi-igenomes/igenomes//Gallus_gallus/UCSC/galGal4/Annotation/Genes/genes.gtf", "bed12": "s3://ngi-igenomes/igenomes//Gallus_gallus/UCSC/galGal4/Annotation/Genes/genes.bed", "readme": "s3://ngi-igenomes/igenomes//Gallus_gallus/UCSC/galGal4/Annotation/README.txt", "mito_name": "chrM" }, "panTro4": { "fasta": "s3://ngi-igenomes/igenomes//Pan_troglodytes/UCSC/panTro4/Sequence/WholeGenomeFasta/genome.fa", "bwa": "s3://ngi-igenomes/igenomes//Pan_troglodytes/UCSC/panTro4/Sequence/BWAIndex/version0.6.0/", "bowtie2": "s3://ngi-igenomes/igenomes//Pan_troglodytes/UCSC/panTro4/Sequence/Bowtie2Index/", "star": "s3://ngi-igenomes/igenomes//Pan_troglodytes/UCSC/panTro4/Sequence/STARIndex/", "bismark": "s3://ngi-igenomes/igenomes//Pan_troglodytes/UCSC/panTro4/Sequence/BismarkIndex/", "gtf": "s3://ngi-igenomes/igenomes//Pan_troglodytes/UCSC/panTro4/Annotation/Genes/genes.gtf", "bed12": "s3://ngi-igenomes/igenomes//Pan_troglodytes/UCSC/panTro4/Annotation/Genes/genes.bed", "readme": "s3://ngi-igenomes/igenomes//Pan_troglodytes/UCSC/panTro4/Annotation/README.txt", "mito_name": "chrM" }, "rn6": { "fasta": "s3://ngi-igenomes/igenomes//Rattus_norvegicus/UCSC/rn6/Sequence/WholeGenomeFasta/genome.fa", "bwa": "s3://ngi-igenomes/igenomes//Rattus_norvegicus/UCSC/rn6/Sequence/BWAIndex/version0.6.0/", "bowtie2": "s3://ngi-igenomes/igenomes//Rattus_norvegicus/UCSC/rn6/Sequence/Bowtie2Index/", "star": "s3://ngi-igenomes/igenomes//Rattus_norvegicus/UCSC/rn6/Sequence/STARIndex/", "bismark": "s3://ngi-igenomes/igenomes//Rattus_norvegicus/UCSC/rn6/Sequence/BismarkIndex/", "gtf": "s3://ngi-igenomes/igenomes//Rattus_norvegicus/UCSC/rn6/Annotation/Genes/genes.gtf", "bed12": "s3://ngi-igenomes/igenomes//Rattus_norvegicus/UCSC/rn6/Annotation/Genes/genes.bed", "mito_name": "chrM" }, "sacCer3": { "fasta": "s3://ngi-igenomes/igenomes//Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/WholeGenomeFasta/genome.fa", "bwa": "s3://ngi-igenomes/igenomes//Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/BWAIndex/version0.6.0/", "bowtie2": "s3://ngi-igenomes/igenomes//Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/Bowtie2Index/", "star": "s3://ngi-igenomes/igenomes//Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/STARIndex/", "bismark": "s3://ngi-igenomes/igenomes//Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/BismarkIndex/", "readme": "s3://ngi-igenomes/igenomes//Saccharomyces_cerevisiae/UCSC/sacCer3/Annotation/README.txt", "mito_name": "chrM", "macs_gsize": "1.2e7" }, "susScr3": { "fasta": "s3://ngi-igenomes/igenomes//Sus_scrofa/UCSC/susScr3/Sequence/WholeGenomeFasta/genome.fa", "bwa": "s3://ngi-igenomes/igenomes//Sus_scrofa/UCSC/susScr3/Sequence/BWAIndex/version0.6.0/", "bowtie2": "s3://ngi-igenomes/igenomes//Sus_scrofa/UCSC/susScr3/Sequence/Bowtie2Index/", "star": "s3://ngi-igenomes/igenomes//Sus_scrofa/UCSC/susScr3/Sequence/STARIndex/", "bismark": "s3://ngi-igenomes/igenomes//Sus_scrofa/UCSC/susScr3/Sequence/BismarkIndex/", "gtf": "s3://ngi-igenomes/igenomes//Sus_scrofa/UCSC/susScr3/Annotation/Genes/genes.gtf", "bed12": "s3://ngi-igenomes/igenomes//Sus_scrofa/UCSC/susScr3/Annotation/Genes/genes.bed", "readme": "s3://ngi-igenomes/igenomes//Sus_scrofa/UCSC/susScr3/Annotation/README.txt", "mito_name": "chrM" } } }