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        Download the raw data used to create the plots in this report below:

        Note that additional data was saved in multiqc_data when this report was generated.

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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 1.25.1

        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/pangenome analysis pipeline. For information about how to interpret these results, please see the documentation.

        Report generated on 2025-01-21, 09:12 UTC based on data in: /home/heumos/git/pangenome/work/0c/5bc476fe46465ab6a0e1dd78b6719d

        ODGI

        Analysis and manipulation of pangenome graphs structured in the variation graph model.URL: https://github.com/pangenome/odgi

        Detailed ODGI stats table.

        Showing 0/1 rows and 10/14 columns.
        Sample NameLengthNodesEdgesPathsComponentsACTGNSelf Loops NodesUnique Self Loops Nodes% GC% N
        DRB1-3123
        36689
        4666
        6386
        12
        2
        10707
        8114
        9500
        7424
        944
        0
        0
        42.4%
        2.6%

        Sum of path node distances

        For each path we iterate from node to node and count the node / nucleotide distance of nodes on the pangenome level normalized by the path length. If a node is reversed, we count the node distance twice.

        This value allows you to evaluate the sorting goodness - how linear the graph is.

        Created with MultiQC

        For each path we iterate from node to node and count the node / nucleotide distance mean_links_length of nodes within the same path only. We then normalized by the path length.

        This value allows you to evaluate the sorting goodness - how linear the graph is.

        DRB1 3123

        Software Versions

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

        GroupSoftwareVersion
        EXTRACT_COMMUNITIESsamtools1.17
        GFAFFIXgfaffix0.1.5b
        NET2COMMUNITIESpggb0.5.4
        ODGI_BUILDodgi0.8.4
        ODGI_DRAW_HEIGHTodgi0.8.4
        ODGI_DRAW_MULTIQCodgi0.8.4
        ODGI_LAYOUTodgi0.8.4
        ODGI_SORTodgi0.8.4
        ODGI_SQUEEZEodgi0.8.4)
        ODGI_STATSodgi0.8.4
        ODGI_UNCHOPodgi0.8.4
        ODGI_VIEWodgi0.8.4
        ODGI_VIZ_COLORodgi0.8.4
        ODGI_VIZ_COMPRodgi0.8.4
        ODGI_VIZ_DEPTHodgi0.8.4
        ODGI_VIZ_INVodgi0.8.4
        ODGI_VIZ_POSodgi0.8.4
        ODGI_VIZ_UNCALLEDodgi0.8.4
        PAF2NETpggb0.5.4
        SAMTOOLS_FAIDXsamtools1.19.2
        SEQWISHseqwish0.7.9
        SMOOTHXGsmoothxg0.8.0
        TABIX_BGZIPtabix1.12
        WFMASH_MAP_ALIGNwfmash0.10.4
        WFMASH_MAP_COMMUNITYwfmash0.10.4
        WorkflowNextflow24.10.3
        nf-core/pangenomev1.2.0dev

        nf-core/pangenome 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/pangenome

        Methods

        Data was processed using nf-core/pangenome v1.2.0dev (doi: 10.5281/zenodo.8202636) 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 v24.10.3 (Di Tommaso et al., 2017) with the following command:

        nextflow run main.nf -profile docker --outdir blue --communities --input ../pggb/data/HLA/DRB1-3123.fa.gz -config conf/hla.config --n_haplotypes 12

        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:
        • 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/pangenome Workflow Summary

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

        Input/output options

        input
        ../pggb/data/HLA/DRB1-3123.fa.gz
        n_haplotypes
        12
        outdir
        blue

        Wfmash Options

        wfmash_map_pct_id
        90.0

        Seqwish Options

        seqwish_sparse_factor
        0.0

        Community

        communities
        true

        Generic options

        trace_report_suffix
        2025-01-21_10-11-47

        Core Nextflow options

        configFiles
        N/A
        containerEngine
        docker
        launchDir
        /home/heumos/git/pangenome
        profile
        docker
        projectDir
        /home/heumos/git/pangenome
        runName
        golden_blackwell
        userName
        heumos
        workDir
        /home/heumos/git/pangenome/work

        MultiQC v1.25.1 - Written by Phil Ewels, available on GitHub.

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