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nf-core/walkercreek: Citations

T. Iverson; UPHL-BioNGS. (2023). WalkerCreek: A Nextflow Pipeline for Influenza Genome Analysis. GitHub repository. https://github.com/UPHL-BioNGS/walkercreek. Accessed December 8, 2023

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

  • 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.

  • abricate

    (https://github.com/StaPH-B/docker-builds/tree/master/abricate/1.0.1-insaflu-220727)

  • irma

    Shepard, S.S., Meno, S., Bahl, J. et al. Viral deep sequencing needs an adaptive approach: IRMA, the iterative refinement meta-assembler. BMC Genomics 17, 708 (2016). https://doi.org/10.1186/s12864-016- 3030-6

  • SRA human read scrubber

    Katz, K.S., Shutov, O., Lapoint, R. et al. STAT: a fast, scalable, MinHash-based k-mer tool to assess Sequence Read Archive next-generation sequence submissions. Genome Biol 22, 270 (2021). https://doi.org/10.1186/s13059-021-02490-0

  • nextclade

    James Hadfield, Colin Megill, Sidney M Bell, John Huddleston, Barney Potter, Charlton Callender, Pavel Sagulenko, Trevor Bedford, Richard A Neher, Nextstrain: real-time tracking of pathogen evolution, Bioinformatics, Volume 34, Issue 23, December 2018, Pages 4121–4123, https://doi.org/10.1093/bioinformatics/bty407

  • bbduk

    https://sourceforge.net/projects/bbmap/

  • faqcs

    Lo CC, Chain PS. Rapid evaluation and quality control of next generation sequencing data with FaQCs. BMC Bioinformatics. 2014 Nov 19;15(1):366. doi: 10.1186/s12859-014-0366-2. PMID: 25408143; PMCID: PMC4246454.

  • kraken2

    Wood, D. E., Lu, J., & Langmead, B. (2019). Improved metagenomic analysis with Kraken 2. Genome Biology, 20(1), 257.

  • seqkit

    W Shen, S Le, Y Li*, F Hu*. SeqKit: a cross-platform and ultrafast toolkit for FASTA/Q file manipulation. PLOS ONE. doi:10.1371/journal.pone.0163962.

Software packaging/containerisation tools

  • 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

  • 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.