software_references_mqc.yaml

        id: 'software_references'
        section_name: 'Software References'
        description: 'This section describes references for the tools used.'
        plot_type: 'html'
        data: |
        
                <h3 id="references">References</h3>
                <ol style="list-style-type: decimal">
                <li><strong>python</strong>:</li>
                </ol>
                <ul>
                <li>Anaconda (Anaconda Software Distribution, <a href="https://anaconda.com" class="uri">https://anaconda.com</a>)</li>
                </ul>
                <ol start="2" style="list-style-type: decimal">
                <li><strong>DERIVA</strong>:</li>
                </ol>
                <ul>
                <li>Bugacov, A., Czajkowski, K., Kesselman, C., Kumar, A., Schuler, R. E. and Tangmunarunkit, H. 2017 Experiences with DERIVA: An Asset Management Platform for Accelerating eScience. IEEE 13th International Conference on e-Science (e-Science), Auckland, 2017, pp. 79-88, doi:<a href="https://doi.org/10.1109/eScience.2017.20">10.1109/eScience.2017.20</a>.</li>
                </ul>
                <ol start="3" style="list-style-type: decimal">
                <li><strong>BDBag</strong>:<br />
                </li>
                </ol>
                <ul>
                <li>D'Arcy, M., Chard, K., Foster, I., Kesselman, C., Madduri, R., Saint, N., &amp; Wagner, R.. 2019. Big Data Bags: A Scalable Packaging Format for Science. Zenodo. doi:<a href="http://doi.org/10.5281/zenodo.3338725">10.5281/zenodo.3338725</a>.</li>
                </ul>
                <ol start="5" style="list-style-type: decimal">
                <li><strong>trimgalore</strong>:</li>
                </ol>
                <ul>
                <li>trimgalore <a href="https://github.com/FelixKrueger/TrimGalore" class="uri">https://github.com/FelixKrueger/TrimGalore</a></li>
                </ul>
                <ol start="6" style="list-style-type: decimal">
                <li><strong>hisat2</strong>:</li>
                </ol>
                <ul>
                <li>Kim ,D.,Paggi, J.M., Park, C., Bennett, C., Salzberg, S.L. 2019 Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol. Aug;37(8):907-915. doi:<a href="https://doi.org/10.1038/s41587-019-0201-4">10.1038/s41587-019-0201-4</a>.</li>
                </ul>
                <ol start="7" style="list-style-type: decimal">
                <li><strong>samtools</strong>:</li>
                </ol>
                <ul>
                <li>Li H., B. Handsaker, A. Wysoker, T. Fennell, J. Ruan, N. Homer, G. Marth, G. Abecasis, R. Durbin, and 1000 Genome Project Data Processing Subgroup. 2009. The Sequence alignment/map (SAM) format and SAMtools. Bioinformatics 25: 2078-9. doi:<a href="http://dx.doi.org/10.1093/bioinformatics/btp352">10.1093/bioinformatics/btp352</a></li>
                </ul>
                <ol start="8" style="list-style-type: decimal">
                <li><strong>picard</strong>:</li>
                </ol>
                <ul>
                <li>“Picard Toolkit.” 2019. Broad Institute, GitHub Repository. <a href="http://broadinstitute.github.io/picard/" class="uri">http://broadinstitute.github.io/picard/</a>; Broad Institute</li>
                </ul>
                <ol start="9" style="list-style-type: decimal">
                <li><strong>featureCounts</strong>:</li>
                </ol>
                <ul>
                <li>Liao, Y., Smyth, G.K., Shi, W. 2014 featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics. Apr 1;30(7):923-30. doi:<a href="https://doi.org/10.1093/bioinformatics/btt656">10.1093/bioinformatics/btt656</a>.</li>
                </ul>
                <ol start="11" style="list-style-type: decimal">
                <li><strong>deeptools</strong>:</li>
                </ol>
                <ul>
                <li>Ramírez, F., D. P. Ryan, B. Grüning, V. Bhardwaj, F. Kilpert, A. S. Richter, S. Heyne, F. Dündar, and T. Manke. 2016. deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic Acids Research 44: W160-165. doi:<a href="http://dx.doi.org/10.1093/nar/gkw257">10.1093/nar/gkw257</a></li>
                </ul>
                <ol start="11" style="list-style-type: decimal">
                <li><strong>Seqtk</strong>:</li>
                </ol>
                <ul>
                <li>Seqtk <a href="https://github.com/lh3/seqtk" class="uri">https://github.com/lh3/seqtk</a></li>
                </ul>
                <ol start="10" style="list-style-type: decimal">