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nf-core/sarek: Citations

nf-core/sarek 3

Hanssen F, Garcia MU, Folkersen L, Pedersen AS, Lescai F, Jodoin S, Miller E, Wacker O, Smith N, nf-core community, Gabernet G, Nahnsen S. Scalable and efficient DNA sequencing analysis on different compute infrastructures aiding variant discovery. bioRxiv. 2023 Jul 19:2023-07.

nf-core/sarek

Garcia MU, Juhos S, Larsson M, Olason PI, Martin M, Eisfeldt J, DiLorenzo S, Sandgren J, Díaz De Ståhl T, Ewels PA, Wirta V, Nistér M, Käller M, Nystedt B. Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants. F1000Res. 2020 Jan 29;9:63. eCollection 2020. doi: 10.12688/f1000research.16665.2. PubMed PMID: 32269765.

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

  • ASCAT

    Van Loo P, Nordgard SH, Lingjærde OC, et al.: Allele-specific copy number analysis of tumors. Proc Natl Acad Sci USA . 2010 Sep 28;107(39):16910-5. doi: 10.1073/pnas.1009843107. PubMed PMID: 20837533; PubMed Central PMCID: PMC2947907.

  • alleleCount

  • 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.

  • BGZip

  • BWA-MEM

    Li H: Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv 2013. doi: 10.48550/arXiv.1303.3997

  • BWA-MEM2

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

  • CNVKIT

    Talevich E, Shain AH, Botton T, Bastian BC (2016) CNVkit: Genome-Wide Copy Number Detection and Visualization from Targeted DNA Sequencing. PLoS Comput Biol 12(4): e1004873. doi: 10.1371/journal.pcbi.1004873. PubMed PMID: 27100738. PubMed Central PMCID: PMC4839673.

  • Control-FREEC

    Boeva V, Popova T, Bleakley K, et al.: Control-FREEC: a tool for assessing copy number and allelic content using next-generation sequencing data. Bioinformatics. 2012; 28(3): 423–5. doi: 10.1093/bioinformatics/btr670. Epub 2011 Dec 6. PubMed PMID: 22155870; PubMed Central PMCID: PMC3268243.

  • dbNSFP

    Liu X, et al.: dbNSFP v4: a comprehensive database of transcript-specific functional predictions and annotations for human nonsynonymous and splice-site SNVs. Genome Med. 2020 Dec 2;12(1):103. doi: 10.1186/s13073-020-00803-9. PubMed PMID: 33261662; PubMed Central PMCID: PMC7709417.

  • DeepVariant

    Poplin, R., Chang, PC., Alexander, D. et al. A universal SNP and small-indel variant caller using deep neural networks. Nat Biotechnol 36, 983–987 (2018). doi: 10.1038/nbt.4235.

  • DragMap

  • 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.

  • FastP

    Shifu Chen, Yanqing Zhou, Yaru Chen, Jia Gu, fastp: an ultra-fast all-in-one FASTQ preprocessor, Bioinformatics, Volume 34, Issue 17, 01 September 2018, Pages i884–i890, doi: 10.1093/bioinformatics/bty560. PubMed PMID: 30423086. PubMed Central PMCID: PMC6129281

  • FastQC

    Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].

  • FGBio

    doi: 10.5281/zenodo.10456900

  • FreeBayes

    Garrison E, Marth G. Haplotype-based variant detection from short-read sequencing. arXiv preprint arXiv:1207.3907 [q-bio.GN] 2012. doi: 10.48550/arXiv.1207.3907

  • GATK

    McKenna A, Hanna M, Banks E, et al.: The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010 Sep;20(9):1297-303. doi: 10.1101/gr.107524.110. Epub 2010 Jul 19. PubMed PMID: 20644199; PubMed Central PMCID: PMC2928508.

  • GNU sed

  • HaplotypeCaller Joint Germline

    Poplin R. et al, Scaling accurate genetic variant discovery to tens of thousands of samples, bioRxiv 2018. doi: 10.1101/201178

  • LOFTEE

    Karczewski KJ, et al.: The mutational constraint spectrum quantified from variation in 141,456 humans. Nature. 2020 May;581(7809):434-443. doi: 10.1038/s41586-020-2308-7. PubMed PMID: 32461654; PubMed Central PMCID: PMC7334197.

  • Manta

    Chen X, Schulz-Trieglaff O, Shaw R, et al.: Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications. Bioinformatics. 2016 Apr 15;32(8):1220-2. doi: 10.1093/bioinformatics/btv710. PubMed PMID: 26647377.

  • Mosdepth

    Brent S Pedersen, Aaron R Quinlan, Mosdepth: quick coverage calculation for genomes and exomes, Bioinformatics, Volume 34, Issue 5, 01 March 2018, Pages 867–868. doi: 10.1093/bioinformatics/btx699. PubMed PMID: 29096012. PubMed Central PMCID: PMC6030888.

  • MSISensorPro

    Peng Jia, Xiaofei Yang, Li Guo, Bowen Liu, Jiadong Lin, Hao Liang, et al. MSIsensor-pro: fast, accurate, and matched-normal-sample-free detection of microsatellite instability. Genomics Proteomics Bioinformatics 2020,18(1). doi: 10.1016/j.gpb.2020.02.001. PubMed PMID: 32171661. PubMed Central PMCID: PMC7393535.

  • 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.

  • PIGZ

  • P7Zip

  • Samblaster

    Gregory G. Faust, Ira M. Hall, SAMBLASTER: fast duplicate marking and structural variant read extraction, Bioinformatics, Volume 30, Issue 17, 1 September 2014, Pages 2503–2505. doi: 10.1093/bioinformatics/btu314. PubMed PMID: 24812344. PubMed Central PMCID: PMC4147885.

  • SAMtools

    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.

  • snpEff

    Cingolani P, Platts A, Wang le L, et al.: A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly (Austin). Apr-Jun 2012;6(2):80-92. doi: 10.4161/fly.19695. PubMed PMID: 22728672; PubMed Central PMCID: PMC3679285.

  • SpliceAI

    Jaganathan K, et al.: Predicting Splicing from Primary Sequence with Deep Learning. Cell. 2019 Jan 24;176(3):535-548.e24. doi: 10.1016/j.cell.2018.12.015. PubMed PMID: 30661751.

  • SpliceRegion

  • Strelka2

    Kim S, Scheffler K, Halpern AL, et al.: Strelka2: fast and accurate calling of germline and somatic variants. Nat Methods. 2018 Aug;15(8):591-594. doi: 10.1038/s41592-018-0051-x. Epub 2018 Jul 16. PubMed PMID: 30013048.

  • SVDB

  • 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.

  • TIDDIT

    Eisfeldt J, Vezzi F, Olason P, et al.: TIDDIT, an efficient and comprehensive structural variant caller for massive parallel sequencing data. F1000Res. 2017 May 10;6:664. doi: 10.12688/f1000research.11168.2. eCollection 2017. PubMed PMID: 28781756; PubMed Central PMCID: PMC5521161.

  • 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.

  • Lofreq

    Wilm et al. LoFreq: A sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets. Nucleic Acids Res. 2012; 40(22):11189-201.

R packages

  • R

    R Core Team (2017). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.

  • RColorBrewer

    Erich Neuwirth (2014). RColorBrewer: ColorBrewer Palettes.

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.