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cdcgov/phoenix: Citations

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

  • BBmap

    BBMap – Bushnell B. – sourceforge.net/projects/bbmap/

  • FastP

    Chen, S., Zhou, Y., Chen, Y., & Gu, J. (2018). Fastp: An ultra-fast all-in-one FASTQ preprocessor. Bioinformatics, 34(17), i884–i890. https://doi.org/10.1093/bioinformatics/bty560

  • Kraken2

    Wood, D. E., Lu, J., & Langmead, B. (2019). Improved metagenomic analysis with Kraken 2. Genome Biology, 20(1), 1–13. https://doi.org/10.1186/s13059-019-1891-0

  • SRST2

    Inouye, M., Dashnow, H., Raven, L. A., Schultz, M. B., Pope, B. J., Tomita, T., Zobel, J., & Holt, K. E. (2014). SRST2: Rapid genomic surveillance for public health and hospital microbiology labs. Genome Medicine, 6(11), 1–16. https://doi.org/10.1186/s13073-014-0090-6

  • SPAdes

    Prjibelski A., Antipov D., Meleshko D., Lapidus A., Korobeynikov A. (2020). Using SPAdes De Novo Assembler. Current protocols in bioinformatics, 70(1), 1934-3396. doi.org/10.1002/cpbi.102.

  • GAMMA

    Stanton, R. A., Vlachos, N., & Halpin, A. L. (2022). GAMMA: a tool for the rapid identification, classification and annotation of translated gene matches from sequencing data. Bioinformatics, 38(2), 546–548. https://doi.org/10.1093/bioinformatics/btab607

  • MLST

    The mlst software incorporates components of the PubMLST database which must be cited in any publications that use mlst: "This publication made use of the PubMLST website (https://pubmlst.org/) developed by Keith Jolley (Jolley & Maiden 2010, BMC Bioinformatics, 11:595) and sited at the University of Oxford. The development of that website was funded by the Wellcome Trust".

    You should also cite this software (currently unpublished) as: Seemann T, mlst Github https://github.com/tseemann/mlst

  • BUSCO

    The novelties introduced in BUSCO v4 and v5 and the new BUSCO datasets (*_odb10) are described here. If you've used these versions the correct citation would be:

    Mosè Manni, Matthew R Berkeley, Mathieu Seppey, Felipe A Simão, Evgeny M Zdobnov, BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes. Molecular Biology and Evolution, Volume 38, Issue 10, October 2021, Pages 4647–4654

    The following protocol covers the various BUSCO running modes and workflows, BUSCO setup, guidelines to interpret the results, and additional analyses, e.g., for building phylogenomic trees and visualizing syntenies using BUSCO results:

    Manni, M., Berkeley, M. R., Seppey, M., & Zdobnov, E. M. (2021). BUSCO: Assessing genomic data quality and beyond. Current Protocols, 1, e323. doi: 10.1002/cpz1.323

  • QUAST

    Mikheenko, A., Prjibelski, A., Saveliev, V., Antipov, D., & Gurevich, A. (2018). Versatile genome assembly evaluation with QUAST-LG. Bioinformatics, 34(13), i142–i150. https://doi.org/10.1093/bioinformatics/bty266

  • MASH

    Ondov, B. D., Treangen, T. J., Melsted, P., Mallonee, A. B., Bergman, N. H., Koren, S., & Phillippy, A. M. (2016). Mash: Fast genome and metagenome distance estimation using MinHash. Genome Biology, 17(1), 1–14. https://doi.org/10.1186/s13059-016-0997-x

  • FastANI

    Jain, C., Rodriguez-R, L. M., Phillippy, A. M., Konstantinidis, K. T., & Aluru, S. (2018). High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nature Communications, 9(1), 1–8. https://doi.org/10.1038/s41467-018-07641-9

  • 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

  • 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.