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nf-core/tumourevo: Citations

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.

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.

Pipeline tools

  • BCFTools

    Li H: A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics. 2011 Nov 1;27(21):2987-93. doi: 10.1093/bioinformatics/btr509. PubMed PMID: 21903627; PubMed Central PMCID: PMC3198575.

  • CNAqc

    Antonello, A., Bergamin, R., Calonaci, N. et al. Computational validation of clonal and subclonal copy number alterations from bulk tumor sequencing using CNAqc. Genome Biol 25, 38 (2024). https://doi.org/10.1186/s13059-024-03170-5

  • CTREE

    Caravagna, G., Giarratano, Y., Ramazzotti, D. et al. Detecting repeated cancer evolution from multi-region tumor sequencing data. Nat Methods 15, 707–714 (2018). https://doi.org/10.1038/s41592-018-0108-x

  • EnsemblVEP

    McLaren W, Gil L, Hunt SE, et al.: The Ensembl Variant Effect Predictor. Genome Biol. 2016 Jun 6;17(1):122. doi: 10.1186/s13059-016-0974-4. PubMed PMID: 27268795; PubMed Central PMCID: PMC4893825.

  • mobster

    Caravagna, G., Heide, T., Williams, M.J. et al. Subclonal reconstruction of tumors by using machine learning and population genetics. Nat Genet 52, 898–907 (2020). https://doi.org/10.1038/s41588-020-0675-5

  • PyClone-VI

    Gillis, S., Roth, A. PyClone-VI: scalable inference of clonal population structures using whole genome data. BMC Bioinformatics 21, 571 (2020). https://doi.org/10.1186/s12859-020-03919-2

  • SigProfiler

    Islam SMA, Díaz-Gay M, Wu Y, Barnes M, Vangara R, Bergstrom EN, He Y, Vella M, Wang J, Teague JW, Clapham P, Moody S, Senkin S, Li YR, Riva L, Zhang T, Gruber AJ, Steele CD, Otlu B, Khandekar A, Abbasi A, Humphreys L, Syulyukina N, Brady SW, Alexandrov BS, Pillay N, Zhang J, Adams DJ, Martincorena I, Wedge DC, Landi MT, Brennan P, Stratton MR, Rozen SG, and Alexandrov LB (2022) Uncovering novel mutational signatures by de novo extraction with SigProfilerExtractor. Cell Genomics. doi: 10.1016/j.xgen.2022.100179.

  • SparseSignatures

    Mella L, Lal A, Angaroni F, Maspero D, Piazza R, Sidow A, Antoniotti M, Graudenzi A, Ramazzotti D. SparseSignatures: An R package using LASSO-regularized non-negative matrix factorization to identify mutational signatures from human tumor samples. STAR Protoc. 2022 Sep 16;3(3):101513. doi: 10.1016/j.xpro.2022.101513. Epub 2022 Jul 1. PMID: 35779264; PMCID: PMC9256827.

  • Tabix

    Li H, Tabix: fast retrieval of sequence features from generic TAB-delimited files, Bioinformatics, Volume 27, Issue 5, 1 March 2011, Pages 718–719, doi: 10.1093/bioinformatics/btq671. PubMed PMID: 21208982. PubMed Central PMCID: PMC3042176.

  • TINC

    Mitchell, J., Milite, S., Bartram, J. et al. Clinical application of tumour-in-normal contamination assessment from whole genome sequencing. Nat Commun 15, 323 (2024). https://doi.org/10.1038/s41467-023-44158-2

  • VIBER

    Caravagna, G., Heide, T., Williams, M.J. et al. Subclonal reconstruction of tumors by using machine learning and population genetics. Nat Genet 52, 898–907 (2020). https://doi.org/10.1038/s41588-020-0675-5

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.