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nw-page/bigbacter: 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;38(3):276-278. doi: 10.1038/s41587-020-0439-x. PMID: 32055031.

Nextflow

Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C. Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017;35(4):316-319. doi: 10.1038/nbt.3820. PMID: 28398311.

Pipeline tools

Sequence retrieval and preprocessing

  • NCBI Sequence Read Archive / SRA Toolkit

    Leinonen R, Sugawara H, Shumway M; International Nucleotide Sequence Database Collaboration. The Sequence Read Archive. Nucleic Acids Res. 2011;39(Database issue):D19-D21. doi: 10.1093/nar/gkq1019. PMID: 21062823; PMCID: PMC3013647.

  • NCBI Datasets

    National Center for Biotechnology Information. NCBI Datasets command-line tools [software]. National Library of Medicine, National Institutes of Health.

  • Seqtk

    Li H. Seqtk: toolkit for processing sequences in FASTA/Q formats [software].

  • FastQC

    Andrews S. FastQC: A Quality Control Tool for High Throughput Sequence Data [software]. 2010.

  • fastp

    Chen S, Zhou Y, Chen Y, Gu J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018;34(17):i884-i890. doi: 10.1093/bioinformatics/bty560. PMID: 30423086; PMCID: PMC6129281.

Genome assembly

  • Shovill

    Seemann T. Shovill: assemble bacterial isolate genomes from Illumina paired-end reads [software]. 2016.

  • SPAdes

    Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012;19(5):455-477. doi: 10.1089/cmb.2012.0021. PMID: 22506599; PMCID: PMC3342519.

Taxonomic identification and clustering

  • GAMBIT

    Lumpe J, Gumbleton L, Gorzalski A, Libuit K, Varghese V, Lloyd T, Tadros F, Arsimendi T, Wagner E, Stephens C, Sevinsky J, Hess D, Pandori M. GAMBIT (Genomic Approximation Method for Bacterial Identification and Tracking): A methodology to rapidly leverage whole genome sequencing of bacterial isolates for clinical identification. PLoS One. 2023;18(2):e0277575. doi: 10.1371/journal.pone.0277575. PMID: 36795668; PMCID: PMC9934365.

  • FLOC

    NW-PaGe. FLOC: MinHash-based genomic clustering software [software].

  • sourmash

    Irber L, Pierce-Ward NT, Abuelanin M, et al. sourmash v4: A multitool to quickly search, compare, and analyze genomic and metagenomic data sets. J Open Source Softw. 2024;9(98):6830. doi: 10.21105/joss.06830.

Variant calling and core-genome analysis

  • Snippy

    Seemann T. Snippy: fast bacterial variant calling from NGS reads [software]. 2015.

  • PolyCore

    NW-PaGe. PolyCore: core-genome alignment and distance analysis software [software].

Recombination detection

  • Gubbins

    Croucher NJ, Page AJ, Connor TR, Delaney AJ, Keane JA, Bentley SD, Parkhill J, Harris SR. Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins. Nucleic Acids Res. 2015;43(3):e15. doi: 10.1093/nar/gku1196. PMID: 25414349; PMCID: PMC4330336.

Phylogenetic inference

  • IQ-TREE 3

    Wong TKF, Ly-Trong N, Ren H, Demotte P, Baños H, Roger AJ, Susko E, Bielow C, De Maio N, Goldman N, Hahn MW, Dos Reis M, Vinh LS, Huttley G, Lanfear R, Minh BQ. IQ-TREE 3: phylogenomic inference software using complex evolutionary models. Mol Biol Evol. 2026;43(5):msag117. doi: 10.1093/molbev/msag117. PMID: 42085559; PMCID: PMC13191116.

Reporting

  • 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(19):3047-3048. doi: 10.1093/bioinformatics/btw354. PMID: 27312411; PMCID: PMC5039924.

Software packaging and containerization

  • Anaconda

    Anaconda Software Distribution [software]. Anaconda, Inc.

  • 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;15(7):475-476. doi: 10.1038/s41592-018-0046-7. 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;33(16):2580-2582. doi: 10.1093/bioinformatics/btx192. PMID: 28379341; PMCID: PMC5870671.

  • Docker

    Merkel D. Docker: lightweight Linux containers for consistent development and deployment. Linux Journal. 2014;2014(239):2.

  • Apptainer / Singularity

    Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017;12(5):e0177459. doi: 10.1371/journal.pone.0177459. PMID: 28494014; PMCID: PMC5426675.