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sanger-tol/variantcalling: Citations

nf-core

Ewels, Philip A., et al. “The Nf-Core Framework for Community-Curated Bioinformatics Pipelines.” Nature Biotechnology, vol. 38, no. 3, Feb. 2020, pp. 276–78, https://doi.org/10.1038/s41587-020-0439-x.

Nextflow

Di Tommaso, Paolo, et al. “Nextflow Enables Reproducible Computational Workflows.” Nature Biotechnology, vol. 35, no. 4, Apr. 2017, pp. 316–19, https://doi.org/10.1038/nbt.3820.

Pipeline tools

  • DeepVariant

    Poplin, Ryan, et al. “A Universal SNP and Small-Indel Variant Caller Using Deep Neural Networks.” Nature Biotechnology, vol. 36, no. 10, 2018, pp. 983–987., https://doi.org/10.1038/nbt.4235.

  • Samtools

    Danecek, Petr, et al. “Twelve Years of SAMtools and BCFtools.” GigaScience, vol. 10, no. 2, Jan. 2021, https://doi.org/10.1093/gigascience/giab008.

  • Bcftools

    Danecek, Petr, et al. “Twelve Years of SAMtools and BCFtools.” GigaScience, vol. 10, no. 2, Jan. 2021, https://doi.org/10.1093/gigascience/giab008.

  • Blast

    Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL. BLAST+: architecture and applications. BMC Bioinformatics. 2009 Dec 15;10:421. doi: 10.1186/1471-2105-10-421. PMID: 20003500; PMCID: PMC2803857.

  • BWA-MEM2

    Vasimuddin Md, Misra S, Li H, Aluru S. Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems. 2019 IEEE International Parallel and Distributed Processing Symposium. 2019 May;314–24. doi: 10.1109/IPDPS.2019.00041.

  • Minimap2

    Li H. New strategies to improve minimap2 alignment accuracy. Bioinformatics. 2021 Oct 8;37(23):4572–4. doi: 10.1093/bioinformatics/btab705. Epub ahead of print. PMID: 34623391; PMCID: PMC8652018.

  • VCFTools

    Danecek P, Auton A, Abecasis G, et al.: The variant call format and VCFtools. Bioinformatics. 2011 Aug 1;27(15):2156-8. doi: 10.1093/bioinformatics/btr330. Epub 2011 Jun 7. PubMed PMID: 21653522; PubMed Central PMCID: PMC3137218.

Software packaging/containerisation tools

  • Anaconda

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

  • Bioconda

    Grüning, Björn, et al. “Bioconda: sustainable and comprehensive software distribution for the life sciences.", Nature Methods, vol. 15, Jul. 2018, pp. 475-6, https://doi.org/10.1038/s41592-018-0046-7.

  • BioContainers

    da Veiga, Felipe, et al. “BioContainers: an open-source and community-driven framework for software standardization.", Bioinformatics, vol. 33, no. 16, Aug. 2017, pp. 2580-2, https://doi.org/10.1093/bioinformatics/btx192.

  • Docker

    Merkel, Dirk, et al. “Docker: Lightweight Linux Containers for Consistent Development and Deployment.", Association for Computing Machinery, vol. 2014, no. 239, Mar. 2014.

  • Singularity

    Kurtzer, Gregory M., et al. “Singularity: Scientific containers for mobility of compute.", PLOS ONE, vol. 12, no. 5, May 2017, pp. e0177459, https://doi.org/10.1371/journal.pone.0177459.