# nf-core/airrflow: 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

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

- [Fastp](https://doi.org/10.1093/bioinformatics/bty560)

  > Shifu Chen, Yanqing Zhou, Yaru Chen, Jia Gu, fastp: an ultra-fast all-in-one FASTQ preprocessor, Bioinformatics. 2018 Sept 1; 34(17):i884–i890. doi: 10.1093/bioinformatics/bty560.

- [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.

- [pRESTO](https://doi.org/10.1093/bioinformatics/btu138)

  > Vander Heiden, J. A., Yaari, G., Uduman, M., Stern, J. N. H., O’Connor, K. C., Hafler, D. A., … Kleinstein, S. H. (2014). pRESTO: a toolkit for processing high-throughput sequencing raw reads of lymphocyte receptor repertoires. Bioinformatics, 30(13), 1930–1932.

- [SHazaM, Change-O](https://doi.org/10.1093/bioinformatics/btv359)

  > Gupta, N. T., Vander Heiden, J. A., Uduman, M., Gadala-Maria, D., Yaari, G., & Kleinstein, S. H. (2015). Change-O: a toolkit for analyzing large-scale B cell immunoglobulin repertoire sequencing data: Table 1. Bioinformatics, 31(20), 3356–3358.

- [Alakazam](https://doi.org/10.1126/scitranslmed.3008879)

  > Stern, J. N. H., Yaari, G., Vander Heiden, J. A., Church, G., Donahue, W. F., Hintzen, R. Q., … O’Connor, K. C. (2014). B cells populating the multiple sclerosis brain mature in the draining cervical lymph nodes. Science Translational Medicine, 6(248).

- [TIgGER](https://doi.org/10.1073/pnas.1417683112)
  > Gadala-maria, D., Yaari, G., Uduman, M., & Kleinstein, S. H. (2015). Automated analysis of high-throughput B-cell sequencing data reveals a high frequency of novel immunoglobulin V gene segment alleles. Proceedings of the National Academy of Sciences, 112(8), 1–9.

## 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.
