# PGScatalog/pgsc_calc: 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

* [PGS Catalog API](https://pubmed.ncbi.nlm.nih.gov/33692568/)
    > Lambert SA, Gil L, Jupp S, Ritchie SC, Xu Y, Buniello A, McMahon A, Abraham G, Chapman M, Parkinson H, Danesh J. The Polygenic Score Catalog as an open database for reproducibility and systematic evaluation. Nature Genetics. 2021 Apr;53(4):420-5. doi: 10.1038/s41588-021-00783-5. PubMed PMID: 33692568.

* [PLINK 1](https://pubmed.ncbi.nlm.nih.gov/17701901/)
    > Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, Maller J, Sklar P, De Bakker PI, Daly MJ, Sham PC. PLINK: a tool set for whole-genome association and population-based linkage analyses. The American journal of human genetics. 2007 Sep 1;81(3):559-75. doi: 10.1086/519795. PubMed PMID:  17701901. PubMed Central PMCID: PMC1950838.

* [PLINK 2](https://pubmed.ncbi.nlm.nih.gov/25722852/)
    > Chang CC, Chow CC, Tellier LC, Vattikuti S, Purcell SM, Lee JJ. Second-generation PLINK: rising to the challenge of larger and richer datasets. Gigascience. 2015 Dec 1;4(1):s13742-015. doi: 10.1186/s13742-015-0047-8. PubMed PMID: 25722852. PubMed Central PMCID: PMC4342193.

## 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)

* [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.
