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BostonGene/pyigmap: Citations

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.

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.

Pipeline tools

  • ffq

    Gálvez-Merchán Á, Min KHJ, Pachter L, Booeshaghi AS. Metadata retrieval from sequence databases with ffq. Bioinformatics. 2023 Jan 1;39(1):btac667. doi: 10.1093/bioinformatics/btac667. PMID: 36610997; PMCID: PMC9883619.

  • Calib

    Baraa Orabi, Emre Erhan, Brian McConeghy, Stanislav V Volik, Stephane Le Bihan, Robert Bell, Colin C Collins, Cedric Chauve, Faraz Hach; Alignment-free clustering of UMI tagged DNA molecules, Bioinformatics, , bty888, 10.1093/bioinformatics/bty888

  • 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.'

  • SeqKit

    Wei Shen*, Botond Sipos, and Liuyang Zhao. 2024. SeqKit2: A Swiss Army Knife for Sequence and Alignment Processing. iMeta e191. doi:10.1002/imt2.191.

    Wei Shen, Shuai Le, Yan Li*, and Fuquan Hu*. SeqKit: a cross-platform and ultrafast toolkit for FASTA/Q file manipulation. PLOS ONE. doi:10.1371/journal.pone.0163962.

  • Vidjil

    Marc Duez et al., “Vidjil: A web platform for analysis of high-throughput repertoire sequencing”, PLOS ONE 2016, 11(11):e0166126 10.1371/journal.pone.0166126

    Mathieu Giraud, Mikaël Salson, et al., “Fast multiclonal clusterization of V(D)J recombinations from high-throughput sequencing”, BMC Genomics 2014, 15:409 10.1186/1471-2164-15-409

  • IgBLAST

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

  • OLGA

    Zachary Sethna, Yuval Elhanati, Curtis G Callan, Aleksandra M Walczak, Thierry Mora, OLGA: fast computation of generation probabilities of B- and T-cell receptor amino acid sequences and motifs, Bioinformatics, Volume 35, Issue 17, September 2019, Pages 2974–2981, 10.1093/bioinformatics/btz035

Software packaging/containerisation tools

  • Docker

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

  • Podman

    Heon, M. et . al . (2018) “Podman - : A tool for managing OCI containers and pods”. Zenodo. doi: 10.5281/zenodo.4735634.