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nf-core/oncoanalyser: Citations

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

  • BCFtools

    Danecek, P., Bonfield, J. K., Liddle, J., Marshall, J., Ohan, V., Pollard, M. O., Whitwham, A., Keane, T., McCarthy, S. A., Davies, R. M., & Li, H. (2021). Twelve years of SAMtools and BCFtools. GigaScience, 10(2), giab008. https://doi.org/10.1093/gigascience/giab008

  • BWA

    Li, H., & Durbin, R. (2009). Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics, 25(14), 1754–1760. https://doi.org/10.1093/bioinformatics/btp324

  • bwa-mem2

    Vasimuddin, Md., Misra, S., Li, H., & Aluru, S. (2019). Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems. 2019 IEEE International Parallel and Distributed Processing Symposium (IPDPS), 314–324. https://doi.org/10.1109/IPDPS.2019.00041

  • CHORD

    Nguyen, L., W. M. Martens, J., Van Hoeck, A., & Cuppen, E. (2020). Pan-cancer landscape of homologous recombination deficiency. Nature Communications, 11(1), 5584. https://doi.org/10.1038/s41467-020-19406-4

  • fastp

    Chen, S., Zhou, Y., Chen, Y., & Gu, J. (2018). fastp: An ultra-fast all-in-one FASTQ preprocessor. Bioinformatics, 34(17), i884–i890. https://doi.org/10.1093/bioinformatics/bty560

  • GATK

    McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., Garimella, K., Altshuler, D., Gabriel, S., Daly, M., & DePristo, M. A. (2010). The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Research, 20(9), 1297–1303. https://doi.org/10.1101/gr.107524.110

  • GRIDSS2

    Cameron, D. L., Baber, J., Shale, C., Valle-Inclan, J. E., Besselink, N., van Hoeck, A., Janssen, R., Cuppen, E., Priestley, P., & Papenfuss, A. T. (2021). GRIDSS2: Comprehensive characterisation of somatic structural variation using single breakend variants and structural variant phasing. Genome Biology, 22(1), Article 1. https://doi.org/10.1186/s13059-021-02423-x

  • LILAC

    Martínez-Jiménez, F., Priestley, P., Shale, C., Baber, J., Rozemuller, E., & Cuppen, E. (2023). Genetic immune escape landscape in primary and metastatic cancer. Nature Genetics, 55(5), 820–831. https://doi.org/10.1038/s41588-023-01367-1

  • LINX

    Shale, C., Cameron, D. L., Baber, J., Wong, M., Cowley, M. J., Papenfuss, A. T., Cuppen, E., & Priestley, P. (2022). Unscrambling cancer genomes via integrated analysis of structural variation and copy number. Cell Genomics, 2(4). https://doi.org/10.1016/j.xgen.2022.100112

  • PURPLE

    Priestley, P., Baber, J., Lolkema, M. P., Steeghs, N., de Bruijn, E., Shale, C., Duyvesteyn, K., Haidari, S., van Hoeck, A., Onstenk, W., Roepman, P., Voda, M., Bloemendal, H. J., Tjan-Heijnen, V. C. G., van Herpen, C. M. L., Labots, M., Witteveen, P. O., Smit, E. F., Sleijfer, S., … Cuppen, E. (2019). Pan-cancer whole-genome analyses of metastatic solid tumours. Nature, 575(7781), 210–216. https://doi.org/10.1038/s41586-019-1689-y

  • Sambamba

    Tarasov, A., Vilella, A. J., Cuppen, E., Nijman, I. J., & Prins, P. (2015). Sambamba: Fast processing of NGS alignment formats. Bioinformatics, 31(12), 2032–2034. https://doi.org/10.1093/bioinformatics/btv098

  • SAMtools

    Danecek, P., Bonfield, J. K., Liddle, J., Marshall, J., Ohan, V., Pollard, M. O., Whitwham, A., Keane, T., McCarthy, S. A., Davies, R. M., & Li, H. (2021). Twelve years of SAMtools and BCFtools. GigaScience, 10(2), giab008. https://doi.org/10.1093/gigascience/giab008

  • STAR

    Dobin, A., Davis, C. A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., Batut, P., Chaisson, M., & Gingeras, T. R. (2013). STAR: Ultrafast universal RNA-seq aligner. Bioinformatics, 29(1), 15–21. https://doi.org/10.1093/bioinformatics/bts635

  • VIRUSBreakend

    Cameron, D. L., Jacobs, N., Roepman, P., Priestley, P., Cuppen, E., & Papenfuss, A. T. (2021). VIRUSBreakend: Viral Integration Recognition Using Single Breakends. Bioinformatics, 37(19), 3115–3119. https://doi.org/10.1093/bioinformatics/btab343

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

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

  • 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.