id: "nf-core-methylseq-methods-description"
description: "Suggested text and references to use when describing pipeline usage within the methods section of a publication."
section_name: "nf-core/methylseq Methods Description"
section_href: "https://github.com/nf-core/methylseq"
plot_type: "html"
data: |
  <h4>Methods</h4>
  <p>Data was processed using nf-core/methylseq v3.0.0 (doi: <a href='https://doi.org/10.5281/zenodo.1343417'>10.5281/zenodo.1343417</a>) of the nf-core collection of workflows (<a href="https://doi.org/10.1038/s41587-020-0439-x">Ewels <em>et al.</em>, 2020</a>), utilising reproducible software environments from the Bioconda (<a href="https://doi.org/10.1038/s41592-018-0046-7">Grüning <em>et al.</em>, 2018</a>) and Biocontainers (<a href="https://doi.org/10.1093/bioinformatics/btx192">da Veiga Leprevost <em>et al.</em>, 2017</a>) projects.</p>
  <p>The pipeline was executed with Nextflow v24.10.6 (<a href="https://doi.org/10.1038/nbt.3820">Di Tommaso <em>et al.</em>, 2017</a>) with the following command:</p>
  <pre><code>nextflow run nf-core/methylseq -c /gscratch/srlab/strigg/bin/uw_hyak_srlab.config --input /gscratch/scrubbed/strigg/analyses/20250714_methylseq_test/samplesheet.csv --outdir /gscratch/scrubbed/strigg/analyses/20250714_methylseq_test --fasta /gscratch/srlab/strigg/GENOMES/Porites_evermanni_v1.fa --em_seq -resume -with-report nf_report.html -with-trace -with-timeline nf_timeline.html --skip_trimming --nomeseq</code></pre>
  <p>Tools used in the workflow included: FastQC (Andrews 2010), Trim Galore! (Krueger) Bismark (Krueger 2011) bwa-meth (Pedersen 2014) Picard (Broad Institute 2019) Qualimap (Okonechnikov 2015) Preseq (Daley 2013) MultiQC (Ewels et al. 2016) .</p>
  <h4>References</h4>
  <ul>
    <li>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: <a href="https://doi.org/10.1038/nbt.3820">10.1038/nbt.3820</a></li>
    <li>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: <a href="https://doi.org/10.1038/s41587-020-0439-x">10.1038/s41587-020-0439-x</a></li>
    <li>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: <a href="https://doi.org/10.1038/s41592-018-0046-7">10.1038/s41592-018-0046-7</a></li>
    <li>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: <a href="https://doi.org/10.1093/bioinformatics/btx192">10.1093/bioinformatics/btx192</a></li>
    <li>Andrews S, (2010) FastQC, URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).</li> <li>Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics , 32(19), 3047–3048. doi: /10.1093/bioinformatics/btw354</li> <li>https://www.bioinformatics.babraham.ac.uk/projects/trim_galore</li> <li>Felix Krueger, Simon R. Andrews, Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications, Bioinformatics, Volume 27, Issue 11, 1 June 2011, Pages 1571–1572, doi: /10.1093/bioinformatics/btr167</li> <li>Pedersen, Brent S. and Eyring, Kenneth and De, Subhajyoti and Yang, Ivana V. and Schwartz, David A. Fast and accurate alignment of long bisulfite-seq reads, arXiv:1401.1129, doi: 10.48550/arXiv.1401.1129</li> <li>Picard Tools, Broad Institute. <http://broadinstitute.github.io/picard/></li> <li>Konstantin Okonechnikov, Ana Conesa, Fernando García-Alcalde, Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data, Bioinformatics, Volume 32, Issue 2, 15 January 2016, Pages 292–294, doi: 10.1093/bioinformatics/btv566</li> <li>Daley, T., Smith, A. Predicting the molecular complexity of sequencing libraries. Nat Methods 10, 325–327 (2013). doi: 10.1038/nmeth.2375</li>
  </ul>
  <div class="alert alert-info">
    <h5>Notes:</h5>
    <ul>
      
      <li>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!</li>
      <li>You should also cite all software used within this run. Check the "Software Versions" of this report to get version information.</li>
    </ul>
  </div>