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nf-core/airrflow: Citations

nf-core/airrflow

nf-core/airrflow: an adaptive immune receptor repertoire analysis workflow employing the Immcantation framework

Gisela Gabernet, Susanna Marquez, Robert Bjornson, Alexander Peltzer, Hailong Meng, Edel Aron, Noah Y. Lee, Cole Jensen, David Ladd, Friederike Hanssen, Simon Heumos, nf-core community, Gur Yaari, Markus C. Kowarik, Sven Nahnsen, Steven H. Kleinstein. BioRxiv. 2024. doi: 10.1101/2024.01.18.576147.

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

  • FastQC

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

  • Fastp

    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.

  • pRESTO

    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

    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.

  • IgBLAST

    Ye J, Ma N, Madden TL, Ostell JM. (2013). IgBLAST: an immunoglobulin variable domain sequence analysis tool. Nucleic Acids Res.

  • Alakazam

    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).

  • SCOPer

    Nouri N, Kleinstein S (2018). “A spectral clustering-based method for identifying clones from high-throughput B cell repertoire sequencing data.” Bioinformatics, i341-i349.

    Nouri N, Kleinstein S (2020). “Somatic hypermutation analysis for improved identification of B cell clonal families from next-generation sequencing data.” PLOS Computational Biology, 16(6), e1007977.

    Gupta N, Adams K, Briggs A, Timberlake S, Vigneault F, Kleinstein S (2017). “Hierarchical clustering can identify B cell clones with high confidence in Ig repertoire sequencing data.” The Journal of Immunology, 2489-2499.

  • Dowser

    Hoehn K, Pybus O, Kleinstein S (2022). “Phylogenetic analysis of migration, differentiation, and class switching in B cells.” PLoS Computational Biology.

  • IgPhyML

    Hoehn K, Van der Heiden J, Zhou J, Lunter G, Pybus O, Kleinstein S (2019). “Repertoire-wide phylogenetic models of B cell molecular evolution reveal evolutionary signatures of aging and vaccination. PNAS, 116(45) 22664-22672."

  • RAxML

    Stamatakis A. (2014) RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics, 30(9): 1312-1313.

  • 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.

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.