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nf-core/ssds: Citations

SSDS method development

Khil P, Smagulova F, Brick K, Camerini-Otero RD, Petukhova G. Sensitive mapping of recombination hotspots using sequencing-based detection of ssDNA. Genome Research. 2012 May;22(5):957-65. doi: 10.1101/gr.130583.111. Epub 2012 Feb 24. PubMed PMID: 22367190; PubMed Central PMCID: PMC3337440.

SSDS for mapping meiotic DSB hotspots

Brick K, Smagulova F, Khil P, Camerini-Otero RD, Petukhova G. Genetic recombination is directed away from functional genomic elements in mice. Nature 2012 May 13;485(7400):642-5. doi: 10.1038/nature11089. PubMed PMID: 22660327; PubMed Central PMCID: PMC3367396.

SSDS for mapping replication origins

Pratto F, Brick K, Cheng G, Lam KWG, Cloutier JM, Dahiya D, Wellard SR, Jordan PW, Camerini-Otero RD. Meiotic recombination mirrors patterns of germline replication in mice and humans. Cell 2021. Aug 5(184;16) 4251-4267. doi: 10.1016/j.cell.2021.06.025 PubMed PMID: 34260899; PubMed Central PMCID: PMC8591710.

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

  • 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.

  • Trimgalore

  • BWA

  • Picard

  • Samtools

  • Parsing SSDS

    Khil P, Smagulova F, Brick K, Camerini-Otero RD, Petukhova G. Sensitive mapping of recombination hotspots using sequencing-based detection of ssDNA. Genome Research. 2012 May;22(5):957-65. doi: 10.1101/gr.130583.111. Epub 2012 Feb 24. PubMed PMID: 22367190; PubMed Central PMCID: PMC3337440.

  • Bedtools

    Quinlan A, Hall I. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010 Mar 15;26(6):841-42. doi: 10.1093/bioinformatics/btq033. PubMed PMID: 20110278; PubMed Central PMCID: PMC2832824.

  • Deeptools

    Ramírez F, Ryan DP, Grüning B, Bhardwaj V, Kilpert F, Richter AS, Heyne S, Dündar F, Manke T. deepTools2: A next Generation Web Server for Deep-Sequencing Data Analysis. Nucleic Acids Research (2016). doi:10.1093/nar/gkw257

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.