# nf-core/raredisease: Citations

## [nf-core](https://pubmed.ncbi.nlm.nih.gov/32055031/)

> 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](https://pubmed.ncbi.nlm.nih.gov/28398311/)

> 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](https://academic.oup.com/gigascience/article/10/2/giab008/6137722) & [SAMtools](https://academic.oup.com/bioinformatics/article/25/16/2078/204688)

  > Danecek P, Bonfield JK, Liddle J, et al. Twelve years of SAMtools and BCFtools. GigaScience. 2021;10(2):giab008. doi:10.1093/gigascience/giab008

- [BWA-MEM](https://arxiv.org/abs/1303.3997)

  > Li H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. Published online May 26, 2013. Accessed March 14, 2023. http://arxiv.org/abs/1303.3997

- [BWA-MEM2](https://ieeexplore.ieee.org/abstract/document/8820962)

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

- [CADD<sup>1</sup>](https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-021-00835-9)<sup>,</sup> [<sup>2</sup>](https://academic.oup.com/nar/article/47/D1/D886/5146191)

  > Rentzsch P, Schubach M, Shendure J, Kircher M. CADD-Splice—improving genome-wide variant effect prediction using deep learning-derived splice scores. Genome Med. 2021;13(1):31. doi:10.1186/s13073-021-00835-9

  > Rentzsch P, Witten D, Cooper GM, Shendure J, Kircher M. CADD: predicting the deleteriousness of variants throughout the human genome. Nucleic Acids Research. 2019;47(D1):D886-D894. doi:10.1093/nar/gky1016

- [DeepVariant](https://www.nature.com/articles/nbt.4235)

  > Poplin R, Chang PC, Alexander D, et al. A universal SNP and small-indel variant caller using deep neural networks. Nat Biotechnol. 2018;36(10):983-987. doi:10.1038/nbt.4235

- [eKLIPse](https://www.nature.com/articles/s41436-018-0350-8)

  > Goudenège D, Bris C, Hoffmann V, et al. eKLIPse: a sensitive tool for the detection and quantification of mitochondrial DNA deletions from next-generation sequencing data. Genet Med 21, 1407–1416 (2019). doi:10.1038/s41436-018-0350-8

- [Ensembl VEP](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0974-4)

  > McLaren W, Gil L, Hunt SE, et al. The Ensembl Variant Effect Predictor. Genome Biol. 2016;17(1):122. doi:10.1186/s13059-016-0974-4

- [ExpansionHunter](https://academic.oup.com/bioinformatics/article/doi/10.1093/bioinformatics/btz431/5499079)

  > Dolzhenko E, Deshpande V, Schlesinger F, et al. ExpansionHunter: a sequence-graph-based tool to analyze variation in short tandem repeat regions. Birol I, ed. Bioinformatics. 2019;35(22):4754-4756. doi:10.1093/bioinformatics/btz431

- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)

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

- [Fastp](https://github.com/OpenGene/fastp)

  > Shifu, C. (2023). Ultrafast one-pass FASTQ data preprocessing, quality control, and deduplication using fastp. iMeta 2: e107. https://doi.org/10.1002/imt2.107

- [GATK](https://genome.cshlp.org/content/20/9/1297)

  > 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;20(9):1297-1303. doi:10.1101/gr.107524.110

- [Genmod](https://github.com/Clinical-Genomics/genmod)

  > Magnusson M, Hughes T, Glabilloy, Bitdeli Chef. genmod: Version 3.7.3. Published online November 15, 2018. doi:10.5281/ZENODO.3841142

- [Gens](https://github.com/Clinical-Genomics-Lund/gens)

- [GLnexus](https://academic.oup.com/bioinformatics/article/36/24/5582/6064144)

  > Yun T, Li H, Chang PC, Lin MF, Carroll A, McLean CY. Accurate, scalable cohort variant calls using DeepVariant and GLnexus. Robinson P, ed. Bioinformatics. 2021;36(24):5582-5589. doi:10.1093/bioinformatics/btaa1081

- [Haplocheck](https://genome.cshlp.org/content/31/2/309.long)

  > Weissensteiner H, Forer L, Fendt L, et al. Contamination detection in sequencing studies using the mitochondrial phylogeny. Genome Res. 2021;31(2):309-316. doi:10.1101/gr.256545.119

- [HaploGrep 2](https://academic.oup.com/nar/article/44/W1/W58/2499296)

  > Weissensteiner H, Pacher D, Kloss-Brandstätter A, et al. HaploGrep 2: mitochondrial haplogroup classification in the era of high-throughput sequencing. Nucleic Acids Res. 2016;44(W1):W58-W63. doi:10.1093/nar/gkw233

- [Hmtnote](https://doi.org/10.1101/600619)

  > Preste R, Clima R, Attimonelli M. Human mitochondrial variant annotation with HmtNote. bioRxiv 600619; doi:10.1101/600619

- [Manta](https://academic.oup.com/bioinformatics/article/32/8/1220/1743909?login=true)

  > 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;32(8):1220-1222. doi:10.1093/bioinformatics/btv710

- [Mosdepth](https://academic.oup.com/bioinformatics/article/34/5/867/4583630?login=true)

  > Pedersen BS, Quinlan AR. Mosdepth: quick coverage calculation for genomes and exomes. Hancock J, ed. Bioinformatics. 2018;34(5):867-868. doi:10.1093/bioinformatics/btx699

- [ngs-bits-samplegender](https://github.com/imgag/ngs-bits/tree/master)

- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)

  > 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.

- [Peddy](<https://www.cell.com/action/showFullTextImages?pii=S0002-9297(17)30017-4>)

  > Pedersen BS, Quinlan AR. Who’s Who? Detecting and Resolving Sample Anomalies in Human DNA Sequencing Studies with Peddy. The American Journal of Human Genetics. 2017;100(3):406-413. doi:10.1016/j.ajhg.2017.01.017

- [Picard](https://broadinstitute.github.io/picard/)

- [Qualimap](https://academic.oup.com/bioinformatics/article/32/2/292/1744356?login=true)

  > Okonechnikov K, Conesa A, García-Alcalde F. Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data. Bioinformatics. 2016;32(2):292-294. doi:10.1093/bioinformatics/btv566

- [RetroSeq](https://academic.oup.com/bioinformatics/article/29/3/389/257479)

  > Thomas M. Keane, Kim Wong, David J. Adams, RetroSeq: transposable element discovery from next-generation sequencing data. Bioinformatics.2013 Feb 1;29(3):389-90. doi: 10.1093/bioinformatics/bts697

- [rhocall](https://github.com/dnil/rhocall)

- [RTG Tools (vcfeval)](https://github.com/RealTimeGenomics/rtg-tools)

  > John G. Cleary, Ross Braithwaite, Kurt Gaastra, Brian S. Hilbush, Stuart Inglis, Sean A. Irvine, Alan Jackson, Richard Littin, Mehul Rathod, David Ware, Justin M. Zook, Len Trigg, and Francisco M. De La Vega. "Comparing Variant Call Files for Performance Benchmarking of Next-Generation Sequencing Variant Calling Pipelines." bioRxiv, 2015. doi:10.1101/023754.

- [Sentieon DNAscope](https://www.biorxiv.org/content/10.1101/2022.05.20.492556v1.abstract)

  > Freed D, Pan R, Chen H, Li Z, Hu J, Aldana R. DNAscope: High Accuracy Small Variant Calling Using Machine Learning. Bioinformatics; 2022. doi:10.1101/2022.05.20.492556

- [Sentieon DNASeq](https://www.frontiersin.org/articles/10.3389/fgene.2019.00736/full)

  > Kendig KI, Baheti S, Bockol MA, et al. Sentieon DNASeq Variant Calling Workflow Demonstrates Strong Computational Performance and Accuracy. Front Genet. 2019;10:736. doi:10.3389/fgene.2019.00736

- [SMNCopyNumberCaller](https://www.nature.com/articles/s41436-020-0754-0)

  > Chen X, Sanchis-Juan A, French CE, Connel AJ, Delon I, Kingsbury Z, Chawla A, Halpern AL, Taft RJ, NIHR BioResource, Bentley DR, Butchbach MER, Raymond FL, Eberle MA. Spinal muscular atrophy diagnosis and carrier screening from genome sequencing data. Genet Med. February 2020:1-9. doi:10.1038/s41436-020-0754-0

- [stranger](https://github.com/Clinical-Genomics/stranger)

  > Nilsson D, Magnusson M. moonso/stranger v0.7.1. Published online February 18, 2021. doi:10.5281/ZENODO.4548873

- [svdb](https://github.com/J35P312/SVDB)

  > Eisfeldt J, Vezzi F, Olason P, Nilsson D, Lindstrand A. TIDDIT, an efficient and comprehensive structural variant caller for massive parallel sequencing data. F1000Res. 2017;6:664. doi:10.12688/f1000research.11168.2

- [Tabix](https://academic.oup.com/bioinformatics/article/27/5/718/262743)

  > Li H. Tabix: fast retrieval of sequence features from generic TAB-delimited files. Bioinformatics. 2011;27(5):718-719. doi:10.1093/bioinformatics/btq671

- [TIDDIT](https://f1000research.com/articles/6-664/v2)

  > Eisfeldt J, Vezzi F, Olason P, Nilsson D, Lindstrand A. TIDDIT, an efficient and comprehensive structural variant caller for massive parallel sequencing data. F1000Res. 2017;6:664. doi:10.12688/f1000research.11168.2

- [UCSC Bigwig and Bigbed](https://academic.oup.com/bioinformatics/article/26/17/2204/199001?login=true)

  > Kent WJ, Zweig AS, Barber G, Hinrichs AS, Karolchik D. BigWig and BigBed: enabling browsing of large distributed datasets. Bioinformatics. 2010;26(17):2204-2207. doi:10.1093/bioinformatics/btq351

- [vcf2cytosure](https://github.com/NBISweden/vcf2cytosure)

- [Vcfanno](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0973-5)

  > Pedersen BS, Layer RM, Quinlan AR. Vcfanno: fast, flexible annotation of genetic variants. Genome Biol. 2016;17(1):118. doi:10.1186/s13059-016-0973-5

## Software packaging/containerisation tools

- [Anaconda](https://anaconda.com)

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

- [Bioconda](https://pubmed.ncbi.nlm.nih.gov/29967506/)

  > 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](https://pubmed.ncbi.nlm.nih.gov/28379341/)

  > 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](https://dl.acm.org/doi/10.5555/2600239.2600241)

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

- [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/)

  > 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.
