IntGenomicsLab/lrsomatic: 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¶
Van Loo P, Nordgard SH, Lingjærde OC, Russnes HG, Rye IH, Sun W, Weigman VJ, Marynen P, Zetterberg A, Naume B, Perou CM, Børresen-Dale AL, Kristensen VN. Allele-specific copy number analysis of tumors. Proc Natl Acad Sci U S A. 2010 Sep 28;107(39):16910-5. doi: 10.1073/pnas.1009843107. Epub 2010 Sep 13. PubMed PMID: 20837533; PubMed Central PMCID: PMC2947907.
Danecek P, Bonfield JK, Liddle J, Marshall J, Ohan V, Pollard MO, Whitwham A, Keane T, McCarthy SA, Davies RM, Li H. Twelve years of SAMtools and BCFtools. Gigascience. 2021 Feb 16;10(2):giab008. doi: 10.1093/gigascience/giab008. PMID: 33590861; PMCID: PMC7931819.
Zheng, Z., Li, S., Su, J. et al. Symphonizing pileup and full-alignment for deep learning-based long-read variant calling. Nat Comput Sci 2, 797–803 (2022). https://doi.org/10.1038/s43588-022-00387-x
Zhenxian Zheng, Junhao Su, Lei Chen, Yan-Lam Lee, Tak-Wah Lam, Ruibang Luo. ClairS: a deep-learning method for long-read somatic small variant calling. bioRxiv 2023.08.17.553778; doi: https://doi.org/10.1101/2023.08.17.553778
Chen L, Zheng Z, Su J, Yu X, Wong AOK, Zhang J, Lee YL, Luo R. ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling. Nat Commun. 2025 Oct 31;16(1):9630. doi: 10.1038/s41467-025-64547-z. PMID: 41173866; PMCID: PMC12579226.
De Coster W. cramino: A fast and simple tool for quality control of long read sequencing data [Software]. GitHub. https://github.com/wdecoster/cramino
McLaren W, Gil L, Hunt SE, Riat HS, Ritchie GR, Thormann A, Flicek P, Cunningham F. 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.
Jha, A., Bohaczuk, S. C., Mao, Y., Ranchalis, J., Mallory, B. J., Min, A. T., Hamm, M. O., Swanson, E., Dubocanin, D., Finkbeiner, C., Li, T., Whittington, D., Noble, W. S., Stergachis, A. B., & Vollger, M. R. (2024). DNA-m6A calling and integrated long-read epigenetic and genetic analysis with fibertools. Genome Research.
Lin JH, Chen LC, Yu SC, Huang YT. LongPhase: an ultra-fast chromosome-scale phasing algorithm for small and large variants. Bioinformatics. 2022 Apr 28;38(9):2452-2455. doi: 10.1093/bioinformatics/btac126. PubMed PMID: 35253834; PubMed Central PMCID: PMC9048675.
Li H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics. 2018 Sep 15;34(18):3094-3100. doi: 10.1093/bioinformatics/bty191. PubMed PMID: 29750242; PubMed Central PMCID: PMC6137996.
Oxford Nanopore Technologies. modkit: A tool for analyzing and manipulating modified base calls [Software]. GitHub. https://github.com/nanoporetech/modkit
Pedersen BS, Quinlan AR. mosdepth: quick coverage calculation for genomes and exomes. Bioinformatics. 2018 Mar 1;34(5):867-868. doi: 10.1093/bioinformatics/btx699. PubMed PMID: 29096012; PubMed Central PMCID: PMC6030888.
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.
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. doi: 10.1093/bioinformatics/btp352. Epub 2009 Jun 8. PubMed PMID: 19505943; PubMed Central PMCID: PMC2723002.
Keskus, A.G., Bryant, A., Ahmad, T. et al. Severus detects somatic structural variation and complex rearrangements in cancer genomes using long-read sequencing. Nat Biotechnol (2025). https://doi.org/10.1038/s41587-025-02618-8
A tool to analyze haplotype-specific chromosome-scale somatic copy number aberrations and aneuploidy using long reads (Oxford Nanopore, PacBio). https://github.com/KolmogorovLab/Wakhan
Software packaging/containerisation tools¶
Anaconda Software Distribution. Computer software. Vers. 2-2.4.0. Anaconda, Nov. 2016. Web.
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.
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.
Merkel, D. (2014). Docker: lightweight linux containers for consistent development and deployment. Linux Journal, 2014(239), 2. doi: 10.5555/2600239.2600241.
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.