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Commit b10c1b1d authored by Venkat Malladi's avatar Venkat Malladi
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Add in yaml files.

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docs/software_references_mqc.yaml 0 → 100644
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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="4" style="list-style-type: decimal">
<li><strong>RSeQC</strong>:</li>
</ol>
<ul>
<li>Wang, L., Wang, S., Li, W. 2012 RSeQC: quality control of RNA-seq experiments. Bioinformatics. Aug 15;28(16):2184-5. doi:<a href="https://doi.org/10.1093/bioinformatics/bts356">10.1093/bioinformatics/bts356</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. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol. 2019 Aug;37(8):907-915. doi: 10.1038/s41587-019-0201-4.</li>
</ul>
<p>Kim D, Paggi JM, Park C, Bennett C, Salzberg SL. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. 2019 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>.</p>
<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="10" style="list-style-type: decimal">
<li><strong>R</strong>:</li>
</ol>
<ul>
<li>R Core Team 2014. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL:<a href="http://www.R-project.org/" class="uri">http://www.R-project.org/</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="12" style="list-style-type: decimal">
<li><strong>FastQC</strong></li>
</ol>
<ul>
<li>FastQC <a href="https://www.bioinformatics.babraham.ac.uk/projects/fastqc/" class="uri">https://www.bioinformatics.babraham.ac.uk/projects/fastqc/</a></li>
</ul>
<ol start="13" style="list-style-type: decimal">
<li><strong>MultiQC</strong>:</li>
</ol>
<ul>
<li>Ewels P., Magnusson M., Lundin S. and Käller M. 2016. MultiQC: Summarize analysis results for multiple tools and samples in a single report. Bioinformatics 32(19): 3047–3048. doi:<a href="https://dx.doi.org/10.1093/bioinformatics/btw354">10.1093/bioinformatics/btw354</a></li>
</ul>
<ol start="14" style="list-style-type: decimal">
<li><strong>Nextflow</strong>:</li>
</ol>
<ul>
<li>Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., and Notredame, C. 2017. Nextflow enables reproducible computational workflows. Nature biotechnology, 35(4), 316.</li>
</ul>
docs/software_versions_mqc.yaml 0 → 100644
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View file @ b10c1b1d
id: 'Software Versions'
section_name: 'Software Versions'
section_href: 'https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/'
plot_type: 'html'
description: 'are collected at run time from the software output.'
data: |
<dl class="dl-horizontal">
<dt>Python</dt><dd>v3.7.7</dd>
<dt>DERIVA</dt><dd>v1.0.0</dd>
<dt>BDBag</dt><dd>v1.5.6</dd>
<dt>RSeQC</dt><dd>v3.0.1</dd>
<dt>Trim Galore!</dt><dd>v0.6.4</dd>
<dt>HISAT2</dt><dd>v2.1.0</dd>
<dt>Samtools</dt><dd>v1.9</dd>
<dt>picard (MarkDuplicates)</dt><dd>v2.23.0-SNAPSHOT</dd>
<dt>featureCounts</dt><dd>v2.0.0</dd>
<dt>R</dt><dd>v3.6.3</dd>
<dt>deepTools</dt><dd>v3.3.2</dd>
<dt>FastQC</dt><dd>v0.11.9</dd>
<dt>MultiQC</dt><dd>v1.8</dd>
<dt>Pipeline Version</dt><dd>v0.0.4_indev</dd>
</dl>
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