Skip to content

Latest commit

 

History

History
76 lines (52 loc) · 4.8 KB

citations.md

File metadata and controls

76 lines (52 loc) · 4.8 KB
Raw

Please cite the following primary sources and databases

Pipeline tools

  • FastQC

    https://www.bioinformatics.babraham.ac.uk/projects/fastqc/

  • PRINSEQ: PReprocessing and INformation of SEQuence data (http://prinseq.sourceforge.net)

    Schmieder R, Edwards R. Quality control and preprocessing of metagenomic datasets. Bioinformatics 2011;27:863–4. doi: 10.1093/bioinformatics/btr026.

  • MultiQC

    Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics 2016;32:3047–8. doi: 10.1093/bioinformatics/btw354.

  • Unicycler

    Wick RR, Judd LM, Gorrie CL, Holt KE. Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLOS Comput Biol 2017;13:e1005595. doi: 10.1371/journal.pcbi.1005595.

  • CheckM

    Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 2015;25:1043–55. doi: 10.1101/gr.186072.114.

  • QUAST

    Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics 2013;29:1072–5. doi: 10.1093/bioinformatics/btt086.

  • GTDB-Tk

    Chaumeil P-A, Mussig AJ, Hugenholtz P, Parks DH. GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. Bioinformatics 2020;36:1925–7. doi: 10.1093/bioinformatics/btz848.

  • PubMLST Server

    Jolley KA, Bray JE, Maiden MCJ. Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications. Wellcome Open Res 2018;3:124. doi: 10.12688/wellcomeopenres.14826.1.

  • CARD Database

    Alcock BP, Huynh W, Chalil R, Smith KW, Raphenya AR, Wlodarski MA, et al. CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database. Nucleic Acids Res 2023;51:D690–9. doi: 10.1093/nar/gkac920.

  • Proksee Server

    Grant JR, Enns E, Marinier E, Mandal A, Herman EK, Chen C, et al. Proksee: in-depth characterization and visualization of bacterial genomes. Nucleic Acids Res 2023;51:W484–92. doi: 10.1093/nar/gkad326.

  • The SEED Server

    Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ, Disz T, et al. The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res 2014;42:D206–14. doi: 10.1093/nar/gkt1226.

  • PHASTER

    Arndt D, Grant JR, Marcu A, Sajed T, Pon A, Liang Y, et al. PHASTER: a better, faster version of the PHAST phage search tool. Nucleic Acids Res 2016;44:W16–21. doi: 10.1093/nar/gkw387.

  • PHAST

    Zhou Y, Liang Y, Lynch KH, Dennis JJ, Wishart DS. PHAST: A Fast Phage Search Tool. Nucleic Acids Res 2011;39:W347–52. doi: 10.1093/nar/gkr485.

  • VFDB 2022

    Liu B, Zheng D, Zhou S, Chen L, Yang J. VFDB 2022: a general classification scheme for bacterial virulence factors. Nucleic Acids Res 2022;50:D912–7. doi: 10.1093/nar/gkab1107.

  • eggNOG 5.0

    Huerta-Cepas J, Szklarczyk D, Heller D, Hernández-Plaza A, Forslund SK, Cook H, et al. eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Res 2019;47:D309–14. doi: 10.1093/nar/gky1085.

  • eggNOG-mapper v2

    Cantalapiedra CP, Hernández-Plaza A, Letunic I, Bork P, Huerta-Cepas J. eggNOG-mapper v2: Functional annotation, orthology assignments, and domain prediction at the metagenomic scale. Mol Biol Evol 2021;38:5825–9. doi: 10.1093/molbev/msab293.

Tools

Databases

Software packaging/containerisation tools

  • Anaconda

  • 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.

    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.