Databases and Bioinformatic Tools Used

NCBI Pathogen Detection Database

The NCBI Pathogen Detection Project. 2016. National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
Available from: https://www.ncbi.nlm.nih.gov/pathogens/

NCBI Sequence Read Archive (SRA)

The NCBI Sequence Read Archive. National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
Available from: https://www.ncbi.nlm.nih.gov/sra/

PubMLST & Achtman 7-gene MLST Scheme

Jolley KA, Bray JE, Maiden MCJ. 2018. Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications. Wellcome Open Res 24;3:124.
PubMed: 30345391 | DOI: 10.12688/wellcomeopenres.14826.1

Achtman M, Wain J, Weill FX, Nair S, Zhou Z, Sangal V, et al. 2012. Multilocus sequence typing as a replacement for serotyping in Salmonella enterica. PLoS Pathog 8(6):e1002776.
PubMed: 22737074 | DOI: 10.1371/journal.ppat.1009040

Bacterial Antimicrobial Resistance Reference Gene Database

Feldgarden M, Brover V, Gonzalez-Escalona N, Frye JG, Haendiges J, et al. 2021. AMRFinderPlus and the Reference Gene Catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence. Sci Rep 11(1):12728.
PubMed: 34135355 | DOI: 10.1038/s41598-021-91456-0

Feldgarden M, Brover V, Fedorov B, et al. 2022. Curation of the AMRFinderPlus databases: applications, functionality and impact. Microb Genom 8(6):mgen000832.
PubMed: 35675101 | DOI: 10.1099/mgen.0.000832

VirulenceDB

Han J, Tang H, Zhao S, Foley SL. 2024. Salmonella enterica virulence databases and bioinformatic analysis tools development. Sci Rep 14(1):25228.
PubMed: 39448688 | DOI: 10.1038/s41598-024-74124-x

PlasmidFinder

Carattoli A, Zankari E, Garcia-Fernandez A, et al. 2014. In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing. Antimicrob Agents Chemother 58:3895−3903.
PubMed: 24777092 | DOI: 10.1128/AAC.02412-14

SPIFinder

Roer L, Hendriksen RS, Leekitcharoenphon P, Lukjancenko O, Kaas RS, Hasman H, Aarestrup FM. 2016. Is the evolution of Salmonella enterica subsp. enterica linked to restriction-modification systems? mSystems 1(3):e00009-16.
PubMed: 27822532 | DOI: 10.1128/mSystems.00009-16

INNUENDO wgMLST Scheme

Rossi M, Silva MSD, Ribeiro-Gonçalves BF, Silva DN, Machado MP, Oleastro M, Borges V, Isidro J, Viera L, Halkilahti J, Jaakkonen A, Palma F, Salmenlinna S, Hakkinen M, Garaizar J, Bikandi J, Hilbert F, Carriço JA. 2018. INNUENDO whole genome and core genome MLST schemas and datasets for Salmonella enterica.
Available from: https://zenodo.org/records/1323684

Alikhan NF, Zhou Z, Sergeant MJ, Achtman M. 2018. A genomic overview of the population structure of Salmonella. PLoS Genet 14(4):e1007261.
PubMed: 29621240 | DOI: 10.1371/journal.pgen.1007261

SRA Toolkit

SRA Toolkit Development Team. 2018. SRA Toolkit [Online].
Available from: https://github.com/ncbi/sra-tools

pigz

Adler M. pigz: a parallel implementation of gzip for modern multi-processor, multi-core machines [Online].
Available from: https://github.com/madler/pigz

fastq-utils

Fonseca N, Manning J. fastq-utils: validation and manipulation of FASTQ files, scRNA-seq barcode pre-processing and UMI quantification [Online].
Available from: https://github.com/nunofonseca/fastq_utils

Trimmomatic

Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114−2120.
PubMed: 24695404 | DOI: 10.1093/bioinformatics/btu170

FastQC

Andrews S. 2010. FastQC: a quality control tool for high throughput sequence data [Online].
Available from: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/

MultiQC

Ewels P, Magnusson M, Lundin S, Käller M. 2016. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics 32(19):3047−3048.
PubMed: 27312411 | DOI: 10.1093/bioinformatics/btw354

Shovill

Seemann T. Shovill [Online].
Available from: https://github.com/tseemann/shovill

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. 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455−477.
PubMed: 22506599 | DOI: 10.1089/cmb.2012.0021

QUAST

Gurevich A, Saveliev V, Vyahhi N, Tesler G. 2013. QUAST: quality assessment tool for genome assemblies. Bioinformatics 29:1072−1075.
PubMed: 23422339 | DOI: 10.1093/bioinformatics/btt086

SeqSero2

Zhang S, den Bakker HC, Li S, Chen J, Dinsmore BA, Lane C, Lauer AC, Fields PI, Deng X. 2019. SeqSero2: rapid and improved Salmonella serotype determination using whole-genome sequencing data. Appl Environ Microbiol 85(23):e01746-19.
PubMed: 31540993 | DOI: 10.1128/AEM.01746-19

Zhang S, Yin Y, Jones MB, Zhang Z, Deatherage Kaiser BL, Dinsmore BA, Fitzgerald C, Fields PI, Deng X. 2015. Salmonella serotype determination utilizing high-throughput genome sequencing data. J Clin Microbiol 53(5):1685−92.
PubMed: 25762776 | DOI: 10.1128/JCM.00323-15

SISTR

Yoshida CE, Kruczkiewicz P, Laing CR, Lingohr EJ, Gannon VP, Nash JH, Taboada EN. 2016. The Salmonella In Silico Typing Resource (SISTR): an open web-accessible tool for rapidly typing and subtyping draft Salmonella genome assemblies. PLoS One 11:e0147101.
PubMed: 26800248 | DOI: 10.1371/journal.pone.0147101

mlst

Seemann T. mlst [Online].
Available from: https://github.com/tseemann/mlst

chewBBACA

Silva M, Machado MP, Silva DN, Rossi M, Moran-Gilad J, Santos S, Ramirez M, Carriço JA. 2018. chewBBACA: A complete suite for gene-by-gene schema creation and strain identification. Microb Genom 4(3):e000166.
PubMed: 29543149 | DOI: 10.1099/mgen.0.000166

cgmlst-dists

Seemann T. cgmlst-dists [Online].
Available from: https://github.com/tseemann/cgmlst-dists

ReporTree

Mixão V, Pinto M, Sobral D, Di Pasquale A, Gomes JP, Borges V. 2023. ReporTree: a surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data. Genome Med 15(1):43.
PubMed: 37322495 | DOI: 10.1186/s13073-023-01196-1

GrapeTree

Zhou Z, Alikhan NF, Sergeant MJ, Luhmann N, Vaz C, Francisco AP, Carrico JA, Achtman M. 2018. GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens. Genome Res 28:1395−1404.
PubMed: 30049790 | DOI: https://doi.org/10.1101/gr.232397.117

AMRFinderPlus

Feldgarden M, Brover V, Gonzalez-Escalona N, Frye JG, Haendiges J, Haft DH, Hoffmann M, Pettengill JB, Prasad AB, Tillman GE, Tyson GH, Klimke W. 2021. AMRFinderPlus and the Reference Gene Catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence. Sci Rep 11(1):12728.
PubMed: 34135355 | DOI: 10.1038/s41598-021-91456-0

ABRicate

Seemann T. ABRicate [Online].
Available from: https://github.com/tseemann/abricate

R & R Packages

R Core Team. 2016. R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.
Available from: https://www.R-project.org/

Barrett T, Dowle M, Srinivasan A, Gorecki J, Chirico M, Hocking T, Schwendinger B. 2024. data.table: Extension of 'data.frame'. [Online].
Available from: https://r-datatable.com

Wickham H, Averick M, Bryan J, Chang W, McGowan LD, François R, Grolemund G, Hayes A, Henry L, Hester J, Kuhn M, Pedersen TL, Miller E, Bache SM, Müller K, Ooms J, Robinson D, Seidel DP, Spinu V, Takahashi K, Vaughan D, Wilke C, Woo K, Yutani H. 2019. Welcome to the tidyverse. J Open Source Softw 4(43): 1686.
DOI: 10.21105/joss.01686