CITATIONS.md

nf-core/methylseq: Citations

nf-core/methylseq

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

nf-core

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

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/

• Trim Galore!

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

• Bismark

  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

• bwa-meth

  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

• Picard

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

• Qualimap

  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

• Preseq

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

• MultiQC

  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.

Software packaging/containerisation tools

• Anaconda

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

• Bioconda

  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

  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

• Singularity

  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.