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        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411
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        Tool Citations

        Please remember to cite the tools that you use in your analysis.

        To help with this, you can download publication details of the tools mentioned in this report:

        About MultiQC

        This report was generated using MultiQC, version 1.28

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/MultiQC/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        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/pairgenomealign analysis pipeline. For information about how to interpret these results, please see the documentation.
        Report generated on 2025-05-09, 13:49 JST based on data in: /flash/LuscombeU/charles-plessy/cache/nf_deleteme/e0/84e5ec4b3b98daeace6e81620ac563

        Training parameter statistics

        Showing 2/2 rows and 6/6 columns.
        idSubstitution Percent IdentityTemperatureGap existenceGap extensionInsertion existenceInsertion extension
        target___test1.train
        100.0
        4.2
        45
        3
        45
        3
        target___test2.train
        100.0
        4.2
        45
        3
        45
        3

        Alignment statistics

        Showing 2/2 rows and 2/2 columns.
        SampleTotal alignment lengthPercent similarity
        target___test1
        29829
        100
        target___test2
        29590
        100.0

        Base frequency

        This plot shows a brief summary of each base content/percentage in the query genomes.

        Created with MultiQC

        Contig length statistics

        This plot shows a short statistics abouth the length of contigs in the query genomes.

        Showing 2/2 rows and 6/6 columns.
        idTOTALcontiglenMINcontiglenMAXcontiglentotalcontigscontigs>1kcontigs>10k
        test1
        29829
        29829
        29829
        1
        1
        1
        test2
        36124
        446
        20973
        5
        3
        1

        Software Versions

        Software Versions lists versions of software tools extracted from file contents.

        GroupSoftwareVersion
        ALIGNMENT_DOTPLOT_O2Olast1608
        ALIGNMENT_LASTAL_M2Olast1608
        ALIGNMENT_LASTDBlast1608
        ALIGNMENT_SPLIT_O2Olast1608
        ALIGNMENT_TRAINlast1608
        ASSEMBLYSCANassemblyscan0.4.1
        CUTN_TARGETseqtk1.4-r122
        WorkflowNextflow24.10.6
        nf-core/pairgenomealignv2.0.0

        nf-core/pairgenomealign 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/pairgenomealign

        Methods

        Data was processed using nf-core/pairgenomealign v2.0.0 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 v24.10.6 (Di Tommaso et al., 2017) with the following command:

        nextflow run . -profile oist,test -w /flash/LuscombeU/charles-plessy/cache/nf_deleteme --outdir test

        References

        • 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
        • 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:
        • If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used.
        • 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/pairgenomealign Workflow Summary

        - this information is collected when the pipeline is started.URL: https://github.com/nf-core/pairgenomealign

        Input/output options

        input
        https://raw.githubusercontent.com/nf-core/test-datasets/pairgenomealign/tests/testsamplesheet.csv
        outdir
        test
        target
        https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/genome.fasta

        Alignment options

        last_split_mismap
        1e-05
        lastal_args
        -C2

        Reference genome options

        fasta
        s3://ngi-igenomes/igenomes//Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/WholeGenomeFasta/genome.fa
        genome
        R64-1-1

        Institutional config options

        config_profile_contact
        OISTs Bioinformatics User Group
        config_profile_description
        The Okinawa Institute of Science and Technology Graduate University (OIST) HPC cluster profile provided by nf-core/configs.
        config_profile_name
        Test profile
        config_profile_url
        https://github.com/nf-core/configs/blob/master/docs/oist.md

        Generic options

        trace_report_suffix
        2025-05-09_13-48-20

        Core Nextflow options

        configFiles
        /home/c/charles-plessy/.nextflow/config, /bucket/.deigo/LuscombeU/live/CharlesPlessy/Nextflow/pairgenomealign/nextflow.config
        containerEngine
        singularity
        launchDir
        /bucket/.deigo/LuscombeU/live/CharlesPlessy/Nextflow/pairgenomealign
        profile
        oist,test
        projectDir
        /bucket/.deigo/LuscombeU/live/CharlesPlessy/Nextflow/pairgenomealign
        runName
        friendly_kay
        userName
        charles-plessy
        workDir
        /flash/LuscombeU/charles-plessy/cache/nf_deleteme

        MultiQC v1.28 - Written by Phil Ewels, available on GitHub.

        This report uses Plotly, jQuery, jQuery UI, Bootstrap and FileSaver.js.