# nf-core/variantbenchmarking: 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.

## [nf-test](https://doi.org/10.1101/2024.05.25.595877)

> Forer, L., & Schönherr, S. (2024). Improving the Reliability and Quality of Nextflow Pipelines with nf-test. bioRxiv. https://doi.org/10.1101/2024.05.25.595877

## [nf-prov](https://github.com/nextflow-io/nf-prov)

## [nf-schema](https://nextflow-io.github.io/nf-schema/latest/)

## Pipeline tools

- [Bcftools](http://samtools.github.io/bcftools/bcftools.html)

> 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. PMID: 19505943; PMCID: PMC2723002.

- [BEDTools](https://bedtools.readthedocs.io/)

> Aaron R. Quinlan, Ira M. Hall, BEDTools: a flexible suite of utilities for comparing genomic features, Bioinformatics, Volume 26, Issue 6, March 2010, Pages 841–842, https://doi.org/10.1093/bioinformatics/btq033

- [bedops](https://bedops.readthedocs.io/en/latest/)

> Shane Neph, M. Scott Kuehn, Alex P. Reynolds, Eric Haugen, Robert E. Thurman, Audra K. Johnson, Eric Rynes, Matthew T. Maurano, Jeff Vierstra, Sean Thomas, Richard Sandstrom, Richard Humbert, John A. Stamatoyannopoulos, BEDOPS: high-performance genomic feature operations, Bioinformatics, Volume 28, Issue 14, July 2012, Pages 1919–1920, https://doi.org/10.1093/bioinformatics/bts277

- [datavzrd](https://datavzrd.github.io/docs/index.html)

- [hap.py](https://www.illumina.com/products/by-type/informatics-products/basespace-sequence-hub/apps/hap-py-benchmarking.html)

- [manta](https://github.com/Illumina/manta/blob/v1.6.0/docs/userGuide/README.md)

> Xiaoyu Chen, Ole Schulz-Trieglaff, Richard Shaw, Bret Barnes, Felix Schlesinger, Morten Källberg, Anthony J. Cox, Semyon Kruglyak, Christopher T. Saunders, Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications, Bioinformatics, Volume 32, Issue 8, April 2016, Pages 1220–1222, https://doi.org/10.1093/bioinformatics/btv710

- [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.

- [picard](https://gatk.broadinstitute.org/hc/en-us/articles/360036712531-CreateSequenceDictionary-Picard)

- [RTG Tools](https://www.realtimegenomics.com/products/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, Francisco M. De La Vega bioRxiv 023754; doi: https://doi.org/10.1101/023754

- [SURVIVOR](https://github.com/fritzsedlazeck/SURVIVOR/wiki)

> Jeffares, D., Jolly, C., Hoti, M. et al. Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast. Nat Commun 8, 14061 (2017). https://doi.org/10.1038/ncomms14061

- [SVanalyzer](https://svanalyzer.readthedocs.io/en/latest/index.html)

- [svtk](https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk)

- [svync](https://github.com/nvnieuwk/svync)

- [tabix](https://www.htslib.org/doc/tabix.html)

> Heng Li, Tabix: fast retrieval of sequence features from generic TAB-delimited files, Bioinformatics, Volume 27, Issue 5, March 2011, Pages 718–719, https://doi.org/10.1093/bioinformatics/btq671

- [truvari](https://github.com/ACEnglish/truvari)

> English, A.C., Menon, V.K., Gibbs, R.A. et al. Truvari: refined structural variant comparison preserves allelic diversity. Genome Biol 23, 271 (2022). https://doi.org/10.1186/s13059-022-02840-6

- [UCSC](http://hgdownload.cse.ucsc.edu/admin/exe)

> Hinrichs AS, Karolchik D, Baertsch R, Barber GP, Bejerano G, Clawson H, Diekhans M, Furey TS, Harte RA, Hsu F et al. The UCSC Genome Browser Database: update 2006. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D590-8.

- [witty.er](https://github.com/Illumina/witty.er)

## R packages

- [ggplot2](https://ggplot2.tidyverse.org/)

> Wickham H (2016). ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York. ISBN 978-3-319-24277-4, https://ggplot2.tidyverse.org.

- [reshape2](https://cran.r-project.org/web/packages/reshape2/index.html)

> Wickham H (2007). “Reshaping Data with the reshape Package.” Journal of Statistical Software, 21(12), 1–20. http://www.jstatsoft.org/v21/i12/.

## Python packages

- [pysam](https://pandas.pydata.org/)

## 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.
