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Update references.yml

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<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>
<li>Bugacov, A., Czajkowski, K., Kesselman, C., Kumar, A., Schuler, R. E., &amp; Tangmunarunkit, H. (2017, October). Experiences with DERIVA: An asset management platform for accelerating eScience. In 2017 IEEE 13th International Conference on e-Science (e-Science) (pp. 79-88). IEEE. 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>
<li>Madduri, R., Chard, K., D’Arcy, M., Jung, S. C., Rodriguez, A., Sulakhe, D., ... &amp; Foster, I. (2019). Reproducible big data science: A case study in continuous FAIRness. PloS one, 14(4), e0213013. doi:<a href="https://doi.org/10.1371/journal.pone.0213013">10.1371/journal.pone.0213013</a>.</li>
</ul>
<ol start="4" style="list-style-type: decimal">
<li><strong>trimgalore</strong>:</li>
......@@ -35,13 +35,13 @@
<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>
<li>Kim, D., Paggi, J. M., Park, C., Bennett, C., &amp; Salzberg, S. L. (2019). Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nature biotechnology, 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="6" 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>
<li>Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., ... &amp; Durbin, R. (2009). The sequence alignment/map format and SAMtools. Bioinformatics, 25(16), 2078-2079. doi:<a href="http://dx.doi.org/10.1093/bioinformatics/btp352">10.1093/bioinformatics/btp352</a></li>
</ul>
<ol start="7" style="list-style-type: decimal">
<li><strong>picard</strong>:</li>
......@@ -53,13 +53,13 @@
<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>
<li>Liao, Y., Smyth, G. K., &amp; Shi, W. (2014). featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics, 30(7), 923-930. doi:<a href="https://doi.org/10.1093/bioinformatics/btt656">10.1093/bioinformatics/btt656</a>.</li>
</ul>
<ol start="9" 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>
<li>Ramírez, F., Ryan, D. P., Grüning, B., Bhardwaj, V., Kilpert, F., Richter, A. S., ... &amp; Manke, T. (2016). deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic acids research, 44(W1), W160-W165. doi:<a href="http://dx.doi.org/10.1093/nar/gkw257">10.1093/nar/gkw257</a></li>
</ul>
<ol start="10" style="list-style-type: decimal">
<li><strong>Seqtk</strong>:</li>
......@@ -83,7 +83,7 @@
<li><strong>SeqWho</strong></li>
</ol>
<ul>
<li>SeqWho <a href="https://git.biohpc.swmed.edu/s181649/seqwho" class="uri">https://git.biohpc.swmed.edu/s181649/seqwho</a></li>
<li>Bennett, C., Thornton, M., Park, C., Henry, G., Zhang, Y., Malladi, V. S., &amp; Kim, D. (2021). SeqWho: Reliable, rapid determination of sequence file identity using k-mer frequencies. bioRxiv, 2021.2003.2010.434827. doi:<a href="https://doi.org/10.1101/2021.03.10.434827">10.1101/2021.03.10.434827</a></li>
</ul>
<ol start="14" style="list-style-type: decimal">
<li><strong>RSeQC</strong>:</li>
......@@ -95,11 +95,11 @@
<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>
<li>Ewels, P., Magnusson, M., Lundin, S., &amp; 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="16" 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>
<li>Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., &amp; Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature biotechnology, 35(4), 316-319.</li>
</ul>
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