# nf-core/methylseq: Citations

## [nf-core/methylseq](https://doi.org/10.5281/zenodo.1343417)

> Phil Ewels, Patrick Hüther, Rickard Hammarén, mashehu, Alexander Peltzer, nf-core bot, Sven F., Johannes Alneberg, Paolo Di Tommaso, Maxime U. Garcia, Colin Davenport, Alessia, Felix Krueger, Guillaume Devailly, Harshil Patel, Robert Syme, VIJAY, & Noirot Céline. (2021). nf-core/methylseq: nf-core/methylseq version 1.6.1 [Nauseous Serpent] (1.6.1). Zenodo. doi: [10.5281/zenodo.4744708](https://doi.org/10.5281/zenodo.4744708)

## [nf-core](https://pubmed.ncbi.nlm.nih.gov/32055031/)

> Ewels PA, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020 Mar;38(3):276-278. doi: 10.1038/s41587-020-0439-x. PubMed PMID: 32055031.

## [Nextflow](https://pubmed.ncbi.nlm.nih.gov/28398311/)

> Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C. Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017 Apr 11;35(4):316-319. doi: 10.1038/nbt.3820. PubMed PMID: 28398311.

## Pipeline tools

- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)

  > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].

- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)

  > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.

- [Trim Galore!](https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/)

  > <https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/>

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- [Bismark](https://doi.org/10.1093/bioinformatics/btr167)

  > 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](https://doi.org/10.1093/bioinformatics/btr167)

- [bwa-meth](https://arxiv.org/abs/1401.1129)

  > 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](https://doi.org/10.48550/arXiv.1401.1129)

- [Picard](http://broadinstitute.github.io/picard/)

  > Picard Tools, Broad Institute. <http://broadinstitute.github.io/picard/>

- [Qualimap](https://doi.org/10.1093/bioinformatics/btv566)

  > 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](https://doi.org/10.1093/bioinformatics/btv566)

- [Preseq](https://doi.org/10.1038/nmeth.2375)

  > Daley, T., Smith, A. Predicting the molecular complexity of sequencing libraries. Nat Methods 10, 325–327 (2013). doi: [10.1038/nmeth.2375](https://doi.org/10.1038/nmeth.2375)

- [Samtools](https://doi.org/10.1093/gigascience/giab008)

  > Petr Danecek, James K Bonfield, Jennifer Liddle, John Marshall, Valeriu Ohan, Martin O Pollard, Andrew Whitwham, Thomas Keane, Shane A McCarthy, Robert M Davies, Heng Li, Twelve years of SAMtools and BCFtools, GigaScience, Volume 10, Issue 2, February 2021, giab008, doi: [10.1093/gigascience/giab008](https://doi.org/10.1093/gigascience/giab008)

- [Bedtools](https://doi.org/10.1093/bioinformatics/btq033)

  > Aaron R. Quinlan, Ira M. Hall, BEDTools: a flexible suite of utilities for comparing genomic features, Bioinformatics, Volume 26, Issue 6, March 2010, Pages 841–842, doi: [10.1093/bioinformatics/btq03](https://doi.org/10.1093/bioinformatics/btq033)

## Software packaging/containerisation tools

- [Anaconda](https://anaconda.com)

  > Anaconda Software Distribution. Computer software. Vers. 2-2.4.0. Anaconda, Nov. 2016. Web.

- [Bioconda](https://pubmed.ncbi.nlm.nih.gov/29967506/)

  > Grüning B, Dale R, Sjödin A, Chapman BA, Rowe J, Tomkins-Tinch CH, Valieris R, Köster J; Bioconda Team. Bioconda: sustainable and comprehensive software distribution for the life sciences. Nat Methods. 2018 Jul;15(7):475-476. doi: 10.1038/s41592-018-0046-7. PubMed PMID: 29967506.

- [BioContainers](https://pubmed.ncbi.nlm.nih.gov/28379341/)

  > da Veiga Leprevost F, Grüning B, Aflitos SA, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Alvarez RV, Griss J, Nesvizhskii AI, Perez-Riverol Y. BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics. 2017 Aug 15;33(16):2580-2582. doi: 10.1093/bioinformatics/btx192. PubMed PMID: 28379341; PubMed Central PMCID: PMC5870671.

- [Docker](https://dl.acm.org/doi/10.5555/2600239.2600241)

  > Merkel, D. (2014). Docker: lightweight linux containers for consistent development and deployment. Linux Journal, 2014(239), 2. doi: 10.5555/2600239.2600241.

- [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/)

  > Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675.
