workflows:
  bactopia:
    name: Bactopia
    link: https://bactopia.github.io/
    description: An extensive workflow to process Nanopore and Illumina sequencing for bacterial genomes
    cite: |
      Petit III RA, Read TD [Bactopia - a flexible pipeline for complete analysis of bacterial genomes.](https://doi.org/10.1128/mSystems.00190-20) _mSystems_ 5 (2020)

  staphopia:
    name: Staphopia
    link: https://staphopia.emory.edu
    description: Staphopia is a flexible pipeline for complete analysis of _Staphylococcus aureus_ genomes.
    cite: |
      Petit III RA, Read TD [_Staphylococcus aureus_ viewed from the perspective of 40,000+ genomes.](http://dx.doi.org/10.7717/peerj.5261) _PeerJ_ 6, e5261 (2018)

datasets_ariba:
  arg_annot:
    name: ARG-ANNOT
    link: http://en.mediterranee-infection.com/article.php?laref=283%26titre=arg-annot
    cite: |
      Gupta SK, Padmanabhan BR, Diene SM, Lopez-Rojas R, Kempf M, Landraud L, Rolain J-M [ARG-ANNOT, a new bioinformatic tool to discover antibiotic resistance genes in bacterial genomes.](https://doi.org/10.1128/aac.01310-13) _Antimicrob. Agents Chemother_ 58, 212–220 (2014)

  card:
    name: CARD
    link: https://card.mcmaster.ca/
    cite: |
      Alcock BP, Raphenya AR, Lau TTY, Tsang KK, Bouchard M, Edalatmand A, Huynh W, Nguyen A-L V, Cheng AA, Liu S, Min SY, Miroshnichenko A, Tran H-K, Werfalli RE, Nasir JA, Oloni M, Speicher DJ, Florescu A, Singh B, Faltyn M, Hernandez-Koutoucheva A, Sharma AN, Bordeleau E, Pawlowski AC, Zubyk HL, Dooley D, Griffiths E, Maguire F, Winsor GL, Beiko RG, Brinkman FSL, Hsiao WWL, Domselaar GV, McArthur AG [CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database.](https://doi.org/10.1093/nar/gkz935) _Nucleic acids research_ 48.D1, D517-D525 (2020)

  ecoh:
    name: EcOH
    link: https://dx.doi.org/10.1099%2Fmgen.0.000064
    cite: |
      Ingle DJ, Valcanis M, Kuzevski A, Tauschek M, Inouye M, Stinear T, Levine MM, Robins-Browne RM, Holt KE [In silico serotyping of E. coli from short read data identifies limited novel O-loci but extensive diversity of O:H serotype combinations within and between pathogenic lineages.](https://doi.org/10.1099/mgen.0.000064) _Microbial Genomics_, 2(7), e000064. (2016)

  megares:
    name: MEGARes
    link: https://megares.meglab.org/
    cite: |
      Lakin SM, Dean C, Noyes NR, Dettenwanger A, Ross AS, Doster E, Rovira P, Abdo Z, Jones KL, Ruiz J, Belk KE, Morley PS, Boucher C [MEGARes: an antimicrobial resistance database for high throughput sequencing.](https://doi.org/10.1093/nar/gkw1009) _Nucleic Acids Res._ 45, D574–D580 (2017)

  megares2:
    name: MEGARes 2.0
    link: https://megares.meglab.org/
    cite: |
      Doster E, Lakin SM, Dean CJ, Wolfe C, Young JG, Boucher C, Belk KE, Noyes NR, Morley PS [MEGARes 2.0: a database for classification of antimicrobial drug, biocide and metal resistance determinants in metagenomic sequence data.](https://doi.org/10.1093/nar/gkz1010) _Nucleic Acids Research_, 48(D1), D561–D569. (2020)

  ncbi_reference_gene_catolog:
    name: NCBI Reference Gene Catalog
    link: https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA313047
    cite: |
      Feldgarden M, Brover V, Haft DH, Prasad AB, Slotta DJ, Tolstoy I, Tyson GH, Zhao S, Hsu C-H, McDermott PF, Tadesse DA, Morales C, Simmons M, Tillman G, Wasilenko J, Folster JP, Klimke W [Validating the NCBI AMRFinder Tool and Resistance Gene Database Using Antimicrobial Resistance Genotype-Phenotype Correlations in a Collection of NARMS Isolates](https://doi.org/10.1128/AAC.00483-19). _Antimicrob. Agents Chemother._ (2019)

  plasmidfinder:
    name: PlasmidFinder
    link: https://cge.cbs.dtu.dk/services/PlasmidFinder/
    cite: |
      Carattoli A, Zankari E, García-Fernández A, Larsen MV, Lund O, Villa L, Aarestrup FM, Hasman H [In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing.](https://doi.org/10.1128/aac.02412-14) _Antimicrob. Agents Chemother._ 58, 3895–3903 (2014)

  resfinder:
    name: ResFinder
    link: https://cge.cbs.dtu.dk//services/ResFinder/
    cite: |
      Zankari E, Hasman H, Cosentino S, Vestergaard M, Rasmussen S, Lund O, Aarestrup FM, Larsen MV [Identification of acquired antimicrobial resistance genes.](https://doi.org/10.1093/jac/dks261) _J. Antimicrob. Chemother._ 67, 2640–2644 (2012)

  srst2:
    name: SRST2
    link: https://github.com/katholt/srst2
    cite: |
      Inouye M, Dashnow H, Raven L-A, Schultz MB, Pope BJ, Tomita T, Zobel J, Holt KE [SRST2: Rapid genomic surveillance for public health and hospital microbiology labs.](https://doi.org/10.1186/s13073-014-0090-6) _Genome Med._ 6, 90 (2014)

  vfdb:
    name: VFDB
    link: http://www.mgc.ac.cn/VFs/
    cite: |
      Chen L, Zheng D, Liu B, Yang J, Jin Q [VFDB 2016: hierarchical and refined dataset for big data analysis--10 years on.](https://doi.org/10.1093/nar/gkv1239) _Nucleic Acids Res._ 44, D694–7 (2016)

  virulencefinder:
    name: VirulenceFinder
    link: https://cge.cbs.dtu.dk/services/VirulenceFinder/
    cite: |
      Joensen KG, Scheutz F, Lund O, Hasman H, Kaas RS, Nielsen EM, Aarestrup FM [Real-time whole-genome sequencing for routine typing, surveillance, and outbreak detection of verotoxigenic _Escherichia coli_.](https://doi.org/10.1128/jcm.03617-13) _J. Clin. Microbiol._ 52, 1501–1510 (2014)

datasets_generic:
  eggnog_db:
    name: eggNOG 5.0 Database
    link: http://eggnog.embl.de/
    cite: | 
      Huerta-Cepas J, Szklarczyk D, Heller D, Hernández-Plaza A, Forslund SK, Cook H, Mende DR, Letunic I, Rattei T, Jensen LJ, von Mering C, Bork P [eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses.](https://doi.org/10.1093/nar/gky1085) _Nucleic Acids Res._ 47, D309–D314 (2019)

  gtdb:
    name: Genome Taxonomy Database
    link: https://gtdb.ecogenomic.org/
    cite: |
      Parks DH, Chuvochina M, Rinke C, Mussig AJ, Chaumeil P-A, Hugenholtz P [GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy](https://doi.org/10.1093/nar/gkab776) _Nucleic Acids Research_ gkab776 (2021)

  mobsuite_db:
    name: MOB-suite Database
    link: https://github.com/phac-nml/mob-suite
    cite: |
      Robertson J, Bessonov K, Schonfeld J, Nash JHE. [Universal whole-sequence-based plasmid typing and its utility to prediction of host range and epidemiological surveillance.](https://doi.org/10.1099/mgen.0.000435) _Microbial Genomics_, 6(10)(2020)

  ncbi_refseq:
    name: NCBI RefSeq Database
    link: https://www.ncbi.nlm.nih.gov/refseq/
    cite: |
      O'Leary NA, Wright MW, Brister JR, Ciufo S, Haddad D, McVeigh R, Rajput B, Robbertse B, Smith-White B, Ako-Adjei D, Astashyn A, Badretdin A, Bao Y, Blinkova O0, Brover V, Chetvernin V, Choi J, Cox E, Ermolaeva O, Farrell CM, Goldfarb T, Gupta T, Haft D, Hatcher E, Hlavina W, Joardar VS, Kodali VK, Li W, Maglott D, Masterson P, McGarvey KM, Murphy MR, O'Neill K, Pujar S, Rangwala SH, Rausch D, Riddick LD, Schoch C, Shkeda A, Storz SS, Sun H, Thibaud-Nissen F, Tolstoy I, Tully RE, Vatsan AR, Wallin C, Webb D, Wu W, Landrum MJ, Kimchi A, Tatusova T, DiCuccio M, Kitts P, Murphy TD, Pruitt KD [Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation.](https://doi.org/10.1093/nar/gkv1189) _Nucleic Acids Res._ 44, D733–45 (2016)

  pubmlst:
    name: PubMLST.org
    link: https://pubmlst.org/
    cite: |
      Jolley KA, Bray JE, Maiden MCJ [Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications.](http://dx.doi.org/10.12688/wellcomeopenres.14826.1) _Wellcome Open Res_ 3, 124 (2018)

  silva:
    name: SILVA rRNA Database
    link: https://www.arb-silva.de/
    cite: |
      Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glöckner FO [The SILVA ribosomal RNA gene database project: improved data processing and web-based tools.](https://doi.org/10.1093/nar/gks1219) _Nucleic Acids Res._ 41, D590–6 (2013)

datasets_minmer:
  mash_refseq:
    name: Mash Refseq (release 88) Sketch
    link: https://mash.readthedocs.io/en/latest/data.html
    cite: |
      Ondov BD, Starrett GJ, Sappington A, Kostic A, Koren S, Buck CB, Phillippy AM [Mash Screen: high-throughput sequence containment estimation for genome discovery](https://doi.org/10.1186/s13059-019-1841-x) _Genome Biol_ 20, 232 (2019)

  sourmash_genbank:
    name: Sourmash Genbank LCA Signature
    link: https://sourmash.readthedocs.io/en/latest/databases.html
    cite: |
      Brown CT, Irber L [sourmash: a library for MinHash sketching of DNA](http://dx.doi.org/10.21105/joss.00027). _JOSS_ 1, 27 (2016)

influences:
    nfcore:
      name: nf-core
      link: https://nf-co.re/
      description: A community effort to collect a curated set of analysis pipelines built using Nextflow.
      cite: |
        Ewels P, 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.](https://dx.doi.org/10.1038/s41587-020-0439-x) _Nat Biotechnol._ (2020)

tools:
  abricate:
    name: Abricate
    link: https://github.com/tseemann/abricate
    description: Mass screening of contigs for antimicrobial and virulence genes
    cite: |
      Seemann T [Abricate: mass screening of contigs for antimicrobial and virulence genes](https://github.com/tseemann/abricate) (GitHub)

  abritamr:
    name: abriTAMR
    link: https://github.com/MDU-PHL/abritamr
    description: A pipeline for running AMRfinderPlus and collating results into functional classes
    cite: |
      Sherry NL, Horan KA, Ballard SA, Gonҫalves da Silva A, Gorrie CL, Schultz MB, Stevens K, Valcanis M, Sait ML, Stinear TP, Howden BP, and Seemann T [An ISO-certified genomics workflow for identification and surveillance of antimicrobial resistance.](https://doi.org/10.1038/s41467-022-35713-4) _Nature Communications_, 14(1), 60. (2023)

  agrvate:
    name: AgrVATE
    link: https://github.com/VishnuRaghuram94/AgrVATE
    description: Rapid identification of Staphylococcus aureus agr locus type and agr operon variants.
    cite: |
      Raghuram V. [AgrVATE: Rapid identification of Staphylococcus aureus agr locus type and agr operon variants.](https://github.com/VishnuRaghuram94/AgrVATE) (GitHub)

  amrfinderplus:
    name: AMRFinderPlus
    link: https://github.com/ncbi/amr
    description: Find acquired antimicrobial resistance genes and some point mutations in protein or assembled nucleotide sequences.
    cite: |
      Feldgarden M, Brover V, Haft DH, Prasad AB, Slotta DJ, Tolstoy I, Tyson GH, Zhao S, Hsu C-H, McDermott PF, Tadesse DA, Morales C, Simmons M, Tillman G, Wasilenko J, Folster JP, Klimke W [Validating the NCBI AMRFinder Tool and Resistance Gene Database Using Antimicrobial Resistance Genotype-Phenotype Correlations in a Collection of NARMS Isolates](https://doi.org/10.1128/AAC.00483-19). _Antimicrob. Agents Chemother._ (2019)

  any2fasta:
    name: any2fasta
    link: https://github.com/tseemann/any2fasta
    description: Convert various sequence formats to FASTA
    cite: | 
      Seemann T [any2fasta: Convert various sequence formats to FASTA](https://github.com/tseemann/any2fasta) (GitHub)

  aragorn:
    name: Aragorn
    link: http://130.235.244.92/ARAGORN/Downloads/
    description: Finds transfer RNA features (tRNA)
    cite: |
      Laslett D, Canback B [ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences.](https://doi.org/10.1093/nar/gkh152) _Nucleic Acids Res_. 32(1):11-6 (2004)

  ariba:
    name: Ariba
    link: https://github.com/sanger-pathogens/ariba
    description: Antimicrobial Resistance Identification By Assembly
    cite: |
      Hunt M, Mather AE, Sánchez-Busó L, Page AJ, Parkhill J, Keane JA, Harris SR [ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads](http://dx.doi.org/10.1099/mgen.0.000131). _Microb Genom_ 3, e000131 (2017)

  art:
    name: ART
    link: https://www.niehs.nih.gov/research/resources/software/biostatistics/art/index.cfm
    description: A set of simulation tools to generate synthetic next-generation sequencing reads
    cite: |
      Huang W, Li L, Myers JR, Marth GT [ART: a next-generation sequencing read simulator.](http://dx.doi.org/10.1093/bioinformatics/btr708) _Bioinformatics_ 28, 593–594 (2012)

  assembly_scan:
    name: assembly-scan
    link: https://github.com/rpetit3/assembly-scan
    description: Generate basic stats for an assembly.
    cite: |
      Petit III RA [assembly-scan: generate basic stats for an assembly](https://github.com/rpetit3/assembly-scan) (GitHub)

  bakta:
    name: Bakta
    link: https://github.com/oschwengers/bakta
    description: Rapid & standardized annotation of bacterial genomes & plasmids
    cite: |
      Schwengers O, Jelonek L, Dieckmann MA, Beyvers S, Blom J, Goesmann A [Bakta - rapid and standardized annotation of bacterial genomes via alignment-free sequence identification.](https://doi.org/10.1099/mgen.0.000685) _Microbial Genomics_ 7(11) (2021)

  barrnap:
    name: Barrnap
    link: https://github.com/tseemann/barrnap
    description: Bacterial ribosomal RNA predictor
    cite: |
      Seemann T [Barrnap: Bacterial ribosomal RNA predictor](https://github.com/tseemann/barrnap) (GitHub)

  bbtools:
    name: BBTools
    link: https://jgi.doe.gov/data-and-tools/bbtools/
    description: BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data.
    cite: |
      Bushnell B [BBMap short read aligner, and other bioinformatic tools.](http://sourceforge.net/projects/bbmap/) (Link)

  bcftools:
    name: BCFtools
    link: https://github.com/samtools/bcftools
    description: Utilities for variant calling and manipulating VCFs and BCFs.
    cite: |
      Danecek P, Bonfield JK, Liddle J, Marshall J, Ohan V, Pollard MO, Whitwham A, Keane T, McCarthy SA, Davies RM, Li H [Twelve years of SAMtools and BCFtools](https://doi.org/10.1093/gigascience/giab008) _GigaScience_ Volume 10, Issue 2 (2021)

  bedtools:
    name: Bedtools
    link: https://github.com/arq5x/bedtools2
    description: A powerful toolset for genome arithmetic.
    cite: |
      Quinlan AR, Hall IM [BEDTools: a flexible suite of utilities for comparing genomic features](http://dx.doi.org/10.1093/bioinformatics/btq033). _Bioinformatics_ 26, 841–842 (2010)

  blast:
    name: BLAST
    link: https://blast.ncbi.nlm.nih.gov/Blast.cgi
    description: Basic Local Alignment Search Tool
    cite: |
      Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL [BLAST+: architecture and applications](http://dx.doi.org/10.1186/1471-2105-10-421). _BMC Bioinformatics_ 10, 421 (2009)

  bowtie2:
    name: Bowtie2
    link: https://github.com/BenLangmead/bowtie2
    description: A fast and sensitive gapped read aligner
    cite: |
      Langmead B, Salzberg SL [Fast gapped-read alignment with Bowtie 2.](http://dx.doi.org/10.1038/nmeth.1923) _Nat. Methods._ 9, 357–359 (2012)

  bracken:
    name: Bracken
    link: https://github.com/jenniferlu717/Bracken
    description: Bracken a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample
    cite: |
      Lu J, Breitwieser FP, Thielen P, and Salzberg SL [Bracken: estimating species abundance in metagenomics data.](https://doi.org/10.7717/peerj-cs.104) _PeerJ Computer Science_, 3, e104. (2017)

  btyper2:
    name: BTyper3
    link: https://github.com/lmc297/BTyper3
    description: In silico taxonomic classification of Bacillus cereus group genomes using whole-genome sequencing data
    cite: |
      Carroll LM, Wiedmann M, Kovac J [Proposal of a Taxonomic Nomenclature for the Bacillus cereus Group Which Reconciles Genomic Definitions of Bacterial Species with Clinical and Industrial Phenotypes.](https://doi.org/10.1128/mBio.00034-20) _mBio_, 11(1). (2020)

  btyper3:
    name: BTyper3
    link: https://github.com/lmc297/BTyper3
    description: In silico taxonomic classification of Bacillus cereus group genomes using whole-genome sequencing data
    cite: |
      Carroll LM, Cheng RA, Kovac J [No Assembly Required: Using BTyper3 to Assess the Congruency of a Proposed Taxonomic Framework for the Bacillus cereus Group With Historical Typing Methods.](https://doi.org/10.3389/fmicb.2020.580691) _Frontiers in Microbiology_, 11, 580691. (2020)

  busco:
    name: BUSCO
    link: https://gitlab.com/ezlab/busco
    description: Assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs (BUSCO)
    cite: |
      Manni M, Berkeley MR, Seppey M, Simão FA, Zdobnov EM [BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes.](https://doi.org/10.1093/molbev/msab199) _Molecular Biology and Evolution_ 38(10), 4647–4654. (2021)

  bwa:
    name: BWA
    link: https://github.com/lh3/bwa/
    description: Burrow-Wheeler Aligner for short-read alignment
    cite: |
      Li H [Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM](http://arxiv.org/abs/1303.3997). _arXiv_ [q-bio.GN] (2013)

  cdhit:
    name: CD-HIT
    link: https://github.com/weizhongli/cdhit
    description: Accelerated for clustering the next-generation sequencing data
    cite: |
      Li W, Godzik A [Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences](http://dx.doi.org/10.1093/bioinformatics/btl158). _Bioinformatics_ 22, 1658–1659 (2006)

  cd_hit_est:
    name: CD-HIT-EST
    link: https://github.com/weizhongli/cdhit
    description: Accelerated for clustering the next-generation sequencing data
    cite: |
      Fu L, Niu B, Zhu Z, Wu S, Li W [CD-HIT: accelerated for clustering the next-generation sequencing data](http://dx.doi.org/10.1093/bioinformatics/bts565). _Bioinformatics_ 28, 3150–3152 (2012)

  checkm:
    name: CheckM
    link: https://github.com/Ecogenomics/CheckM
    description: Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes
    cite: |
      Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW [CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes.](http://dx.doi.org/10.1101/gr.186072.114) _Genome Res_ 25, 1043–1055 (2015)

  clonalframeml:
    name: ClonalFramML
    link: https://github.com/xavierdidelot/ClonalFrameML
    description: Efficient Inference of Recombination in Whole Bacterial Genomes
    cite: |
      Didelot X, Wilson DJ [ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes.](https://doi.org/10.1371/journal.pcbi.1004041) _PLoS Comput Biol_ 11(2) e1004041 (2015)

  csvtk:
    name: csvtk
    link: https://bioinf.shenwei.me/csvtk/
    description: A cross-platform, efficient and practical CSV/TSV toolkit in Golang
    cite: |
      Shen, W [csvtk: A cross-platform, efficient and practical CSV/TSV toolkit in Golang.](https://github.com/shenwei356/csvtk/) (GitHub)

  diamond:
    name: DIAMOND
    link: https://github.com/bbuchfink/diamond
    description: Accelerated BLAST compatible local sequence aligner.
    cite: |
      Buchfink B, Xie C, Huson DH [Fast and sensitive protein alignment using DIAMOND.](http://dx.doi.org/10.1038/nmeth.3176) _Nat. Methods._ 12, 59–60 (2015)

  dragonflye:
    name: Dragonflye
    link: https://github.com/rpetit3/dragonflye
    description: Assemble bacterial isolate genomes from Nanopore reads.
    cite: |
      Petit III RA [Dragonflye: Assemble bacterial isolate genomes from Nanopore reads.](https://github.com/rpetit3/dragonflye) (GitHub)

  ectyper:
    name: ECTyper
    link: https://github.com/phac-nml/ecoli_serotyping
    description: In-silico prediction of _Escherichia coli_ serotype
    cite: Laing C, Bessonov K, Sung S, La Rose C [ECTyper - In silico prediction of _Escherichia coli_ serotype](https://github.com/phac-nml/ecoli_serotyping) (GitHub)

  eggnog_mapper:
    name: eggNOG-mapper
    link: https://github.com/eggnogdb/eggnog-mapper
    description: Fast genome-wide functional annotation through orthology assignment
    cite: |
      Huerta-Cepas J, Forslund K, Coelho LP, Szklarczyk D, Jensen LJ, von Mering C, Bork P [Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper.](http://dx.doi.org/10.1093/molbev/msx148) _Mol. Biol. Evol._ 34, 2115–2122 (2017)

  emmtyper:
    name: emmtyper
    link: https://github.com/MDU-PHL/emmtyper
    description: emm Automatic Isolate Labeller
    cite: |
      Tan A, Seemann T, Lacey D, Davies M, Mcintyre L, Frost H, Williamson D, Gonçalves da Silva A [emmtyper - emm Automatic Isolate Labeller](https://github.com/MDU-PHL/emmtyper) (GitHub)

  fastani:
    name: FastANI
    link: https://github.com/ParBLiSS/FastANI
    description: Fast Whole-Genome Similarity (ANI) Estimation
    cite: |
      Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S [High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries.](http://dx.doi.org/10.1038/s41467-018-07641-9) _Nat. Commun._ 9, 5114 (2018)

  fastqc:
    name: FastQC
    link: https://github.com/s-andrews/FastQC
    description: A quality control analysis tool for high throughput sequencing data.
    cite: |
      Andrews S [FastQC: a quality control tool for high throughput sequence data.](http://www.bioinformatics.babraham.ac.uk/projects/fastqc) (WebLink)

  fastq_dl:
    name: fastq-dl
    link: https://github.com/rpetit3/fastq-dl
    description: Download FASTQ files from SRA or ENA repositories.
    cite: |
      Petit III RA [fastq-dl: Download FASTQ files from SRA or ENA repositories.](https://github.com/rpetit3/fastq-dl) (GitHub)

  fastq_scan:
    name: fastq-scan
    link: https://github.com/rpetit3/fastq-scan
    description: Output FASTQ summary statistics in JSON format
    cite: |
      Petit III RA [fastq-scan: generate summary statistics of input FASTQ sequences.](https://github.com/rpetit3/fastq-scan) (GitHub)

  fastp:
    name: fastp
    link: https://github.com/OpenGene/fastp
    description: A tool designed to provide fast all-in-one preprocessing for FastQ files
    cite: |
      Chen S, Zhou Y, Chen Y, and Gu J [fastp: an ultra-fast all-in-one FASTQ preprocessor.](https://doi.org/10.1093/bioinformatics/bty560) _Bioinformatics_, 34(17), i884–i890. (2018)

  fasttree:
    name: FastTree
    link: http://www.microbesonline.org/fasttree
    description: Approximately-maximum-likelihood phylogenetic trees
    cite: |
      Price MN, Dehal PS, Arkin AP [FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments.](https://dx.doi.org/10.1371%2Fjournal.pone.0009490) _PLoS One_ 5, e9490 (2010)

  flash:
    name: FLASH
    link: https://ccb.jhu.edu/software/FLASH/
    description: A fast and accurate tool to merge paired-end reads.
    cite: |
      Magoč T, Salzberg SL [FLASH: fast length adjustment of short reads to improve genome assemblies.](https://doi.org/10.1093/bioinformatics/btr507) _Bioinformatics_ 27.21 2957-2963 (2011)

  flye:
    name: Flye
    link: https://github.com/fenderglass/Flye
    description: De novo assembler for single molecule sequencing reads using repeat graphs
    cite: |
      Kolmogorov M, Yuan J, Lin Y, Pevzner P [Assembly of Long Error-Prone Reads Using Repeat Graphs](https://doi.org/10.1038/s41587-019-0072-8) _Nature Biotechnology_ (2019)
  
  freebayes:
    name: freebayes
    link: https://github.com/ekg/freebayes
    description: Bayesian haplotype-based genetic polymorphism discovery and genotyping
    cite: |
      Garrison E, Marth G [Haplotype-based variant detection from short-read sequencing.](https://arxiv.org/abs/1207.3907) arXiv preprint arXiv:1207.3907 [q-bio.GN] (2012)

  gamma:
    name: GAMMA
    link: https://github.com/rastanton/GAMMA
    description: Gene Allele Mutation Microbial Assessment
    cite: |
      Stanton RA, Vlachos N, Halpin AL [GAMMA: a tool for the rapid identification, classification, and annotation of translated gene matches from sequencing data.](https://doi.org/10.1093/bioinformatics/btab607) _Bioinformatics_ (2021)

  genotyphi:
    name: GenoTyphi
    link: https://github.com/katholt/genotyphi
    description: Assign genotypes to Salmonella Typhi genomes based on Mykrobe results
    cite: |
      Wong VK, Baker S, Connor TR, Pickard D, Page AJ, Dave J, Murphy N, Holliman R, Sefton A, Millar M, Dyson ZA, Dougan G, Holt KE, & International Typhoid Consortium. [An extended genotyping framework for Salmonella enterica serovar Typhi, the cause of human typhoid](https://doi.org/10.1038/ncomms12827) _Nature Communications_ 7, 12827. (2016)

  gnu_parallel:
    name: GNU Parallel
    link: https://www.gnu.org/software/parallel/
    description: A shell tool for executing jobs in parallel
    cite: |
      Tange O [GNU Parallel](https://doi.org/10.5281/zenodo.1146014) (2018)

  gtdb_tk:
    name: GTDB-Tk
    link: https://github.com/Ecogenomics/GTDBTk
    description: A toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes
    cite: |
      Chaumeil PA, Mussig AJ, Hugenholtz P, Parks DH [GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database.](https://doi.org/10.1093/bioinformatics/btz848) _Bioinformatics_ (2019)

  gubbins:
    name: Gubbins
    link: https://github.com/nickjcroucher/gubbins
    description: Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences
    cite: |
      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.](https://doi.org/10.1093/nar/gku1196) _Nucleic Acids Research_ 43(3), e15. (2015)
  
  hicap:
    name: hicap
    link: https://github.com/scwatts/hicap
    description: in silico typing of the _H. influenzae_ cap locus
    cite: |
      Watts SC, Holt KE [hicap: in silico serotyping of the Haemophilus influenzae capsule locus.](https://doi.org/10.1128/JCM.00190-19) _Journal of Clinical Microbiology_ JCM.00190-19 (2019)

  hmmer:
    name: HMMER
    link: http://hmmer.org/
    description: Biosequence analysis using profile hidden Markov models
    cite: |
      Eddy SR [Accelerated Profile HMM Searches.](https://doi.org/10.1371/journal.pcbi.1002195) _PLoS Comput. Biol._ 7, e1002195 (2011)

  hpsuissero:
    name: HpsuisSero
    link: https://github.com/jimmyliu1326/HpsuisSero
    description: Rapid _Haemophilus parasuis_ serotyping
    cite: |
      Lui J [HpsuisSero: Rapid _Haemophilus parasuis_ serotyping](https://github.com/jimmyliu1326/HpsuisSero) (GitHub)

  infernal:
    name: Infernal
    link: http://eddylab.org/infernal/
    description: Searches DNA sequence databases for RNA structure and sequence similarities
    cite: |
      Nawrocki EP, Eddy SR [Infernal 1.1: 100-fold faster RNA homology searches.](https://doi.org/10.1093/bioinformatics/btt509) _Bioinformatics_ 29(22), 2933-2935 (2013)

  iqtree:
    name: IQ-TREE
    link: https://github.com/Cibiv/IQ-TREE
    description: Efficient phylogenomic software by maximum likelihood
    cite: |
      Nguyen L-T, Schmidt HA, von Haeseler A, Minh BQ [IQ-TREE: A fast and effective stochastic algorithm for estimating maximum likelihood phylogenies.](https://doi.org/10.1093/molbev/msu300) _Mol. Biol. Evol._ 32:268-274 (2015)

  iqtree_modelfinder:
    name: ModelFinder
    link: https://github.com/Cibiv/IQ-TREE
    description: Used for automatic model selection
    cite: |
      Kalyaanamoorthy S, Minh BQ, Wong TKF, von Haeseler A, Jermiin LS [ModelFinder - Fast model selection for accurate phylogenetic estimates.](https://doi.org/10.1038/nmeth.4285) _Nat. Methods_ 14:587-589 (2017)

  iqtree_ufboot:
    name: UFBoot2
    link: https://github.com/Cibiv/IQ-TREE
    description: Used to conduct ultrafast bootstrapping
    cite: |
      Hoang DT, Chernomor O, von Haeseler A, Minh BQ, Vinh LS [UFBoot2: Improving the ultrafast bootstrap approximation.](https://doi.org/10.1093/molbev/msx281) _Mol. Biol. Evol._ 35:518–522 (2018)

  ismapper:
    name: ISMapper
    link: https://github.com/jhawkey/IS_mapper
    description: IS mapping software
    cite: |
      Hawkey J, Hamidian M, Wick RR, Edwards DJ, Billman-Jacobe H, Hall RM, Holt KE [ISMapper: identifying transposase insertion sites in bacterial genomes from short read sequence data](http://dx.doi.org/10.1186/s12864-015-1860-2). _BMC Genomics_ 16, 667 (2015)

  kaptive:
    name: Kaptive
    link: https://github.com/katholt/Kaptive
    description: Surface polysaccharide loci for _Klebsiella pneumoniae_ species complex and _Acinetobacter baumannii_ genomes
    cite: |
      Wyres KL, Wick RR, Gorrie C, Jenney A, Follador R, Thomson NR, Holt KE [Identification of Klebsiella capsule synthesis loci from whole genome data.](https://doi.org/10.1099/mgen.0.000102) _Microbial genomics_ 2(12) (2016)

  kleborate:
    name: Kleborate
    link: https://github.com/katholt/Kleborate
    description: Genotyping tool for _Klebsiella pneumoniae_ and its related species complex
    cite: |
      Lam MMC, Wick RR, Watts, SC, Cerdeira LT, Wyres KL, Holt KE [A genomic surveillance framework and genotyping tool for Klebsiella pneumoniae and its related species complex.](https://doi.org/10.1038/s41467-021-24448-3) _Nat Commun_ 12, 4188 (2021)

  kmc:
    name: KMC
    link: https://github.com/refresh-bio/KMC
    description: Fast and frugal disk based k-mer counter
    cite: |
      Deorowicz S, Kokot M, Grabowski Sz, Debudaj-Grabysz A [KMC 2: Fast and resource-frugal k-mer counting](https://doi.org/10.1093/bioinformatics/btv022) _Bioinformatics_ 31(10):1569–1576 (2015)

  kraken2:
    name: Kraken2
    link: https://github.com/DerrickWood/kraken2
    description: The second version of the Kraken taxonomic sequence classification system
    cite: |
      Wood DE, Lu J, Langmead B [Improved metagenomic analysis with Kraken 2.](https://doi.org/10.1186/s13059-019-1891-0) *Genome Biology*, 20(1), 257. (2019)

  krona:
    name: Krona
    link: https://github.com/marbl/Krona
    description: Interactively explore metagenomes and more from a web browser
    cite: |
      Ondov BD, Bergman NH, and Phillippy AM [Interactive metagenomic visualization in a Web browser.](https://doi.org/10.1186/1471-2105-12-385) _BMC Bioinformatics_, 12, 385. (2011)

  legsta:
    name: legsta
    link: https://github.com/tseemann/legsta
    description: In silico Legionella pneumophila Sequence Based Typing
    cite: | 
      Seemann T [legsta: In silico Legionella pneumophila Sequence Based Typing](https://github.com/tseemann/legsta) (GitHub)

  lighter:
    name: Lighter
    link: https://github.com/mourisl/Lighter
    description: Fast and memory-efficient sequencing error corrector
    cite: |
      Song L, Florea L, Langmead B [Lighter: Fast and Memory-efficient Sequencing Error Correction without Counting](https://doi.org/10.1186/s13059-014-0509-9). _Genome Biol._ 15(11):509 (2014)

  lissero:
    name: LisSero
    link: https://github.com/MDU-PHL/LisSero
    description: _In silico_ serotype prediction for _Listeria monocytogenes_
    cite: |
      Kwong J, Zhang J, Seeman T, Horan, K, Gonçalves da Silva A [LisSero - _In silico_ serotype prediction for _Listeria monocytogenes_](https://github.com/MDU-PHL/LisSero) (GitHub)

  mafft:
    name: MAFFT
    link: https://mafft.cbrc.jp/alignment/software/
    description: Multiple alignment program for amino acid or nucleotide sequences
    cite: |
      Katoh K, Standley DM [MAFFT multiple sequence alignment software version 7: improvements in performance and usability.](https://doi.org/10.1093/molbev/mst010) _Mol. Biol. Evol._ 30, 772–780 (2013)

  mash:
    name: Mash
    link: https://github.com/marbl/Mash
    description: Fast genome and metagenome distance estimation using MinHash
    cite: |
      Ondov BD, Treangen TJ, Melsted P, Mallonee AB, Bergman NH, Koren S, Phillippy AM [Mash: fast genome and metagenome distance estimation using MinHash](http://dx.doi.org/10.1186/s13059-016-0997-x). _Genome Biol_ 17, 132 (2016)

  mash_screen:
    name: Mash
    link: https://github.com/marbl/Mash
    description: High-throughput sequence containment estimation
    cite: |
      Ondov BD, Starrett GJ, Sappington A, Kostic A, Koren S, Buck CB, Phillippy AM [Mash Screen: high-throughput sequence containment estimation for genome discovery](https://doi.org/10.1186/s13059-019-1841-x) _Genome Biol_ 20, 232 (2019)

  mashtree:
    name: Mashtree
    link: https://github.com/lskatz/mashtree
    description: Create a tree using Mash distances
    cite: |
      Katz LS, Griswold T, Morrison S, Caravas J, Zhang S, den Bakker HC, Deng X, Carleton HA [Mashtree: a rapid comparison of whole genome sequence files.](https://doi.org/10.21105/joss.01762) _Journal of Open Source Software_, 4(44), 1762 (2019)

  maskrc_svg:
    name: maskrc-svg
    link: https://github.com/kwongj/maskrc-svg
    description: Masks recombination as detected by ClonalFrameML or Gubbins
    cite: Kwong J [maskrc-svg - Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG.](https://github.com/kwongj/maskrc-svg) (GitHub)

  mccortex:
    name: McCortex
    link: https://github.com/mcveanlab/mccortex
    description: De novo genome assembly and multisample variant calling
    cite: |
      Turner I, Garimella KV, Iqbal Z, McVean G [Integrating long-range connectivity information into de Bruijn graphs.](http://dx.doi.org/10.1093/bioinformatics/bty157) _Bioinformatics_ 34, 2556–2565 (2018)

  mcroni:
    name: mcroni
    link: https://github.com/liampshaw/mcroni
    description: Scripts for finding and processing promoter variants upstream of mcr-1
    cite: |
      Shaw L [mcroni: Scripts for finding and processing promoter variants upstream of mcr-1](https://github.com/liampshaw/mcroni) (GitHub)

  medaka:
    name: Medaka
    link: https://github.com/nanoporetech/medaka
    description: Sequence correction provided by ONT Research
    cite: |
      ONT Research [Medaka: Sequence correction provided by ONT Research](https://github.com/nanoporetech/medaka) (GitHub)
  
  meningotype:
    name: meningotype
    link: https://github.com/MDU-PHL/meningotype
    description: In silico serotyping, finetyping and Bexsero antigen sequence typing of _Neisseria meningitidis_
    cite: |
      Kwong JC, Gonçalves da Silva A, Stinear TP, Howden BP, & Seemann T [meningotype: in silico typing for _Neisseria meningitidis_.](https://github.com/MDU-PHL/meningotype) (GitHub)

  megahit:
    name: MEGAHIT
    link: https://github.com/voutcn/megahit
    description: Ultra-fast and memory-efficient (meta-)genome assembler
    cite: |
      Li D, Liu C-M, Luo R, Sadakane K, Lam T-W [MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.](https://doi.org/10.1093/bioinformatics/btv033) _Bioinformatics_ 31.10 1674-1676 (2015)

  mlst:
    name: mlst
    link: https://github.com/tseemann/mlst
    description: Scan contig files against PubMLST typing schemes
    cite: |
      Seemann T [mlst: scan contig files against PubMLST typing schemes](https://github.com/tseemann/mlst) (GitHub)

  midas:
    name: MIDAS
    link: https://github.com/snayfach/MIDAS
    description: An integrated pipeline for estimating strain-level genomic variation from metagenomic data
    cite: |
      Nayfach S, Rodriguez-Mueller B, Garud N, and Pollard KS [An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography.](https://doi.org/10.1101/gr.201863.115) _Genome Research_, 26(11), 1612–1625. (2016)

  minced:
    name: MinCED
    link: https://github.com/ctSkennerton/minced
    description: Mining CRISPRs in Environmental Datasets
    cite: |
      Skennerton C [MinCED: Mining CRISPRs in Environmental Datasets](https://github.com/ctSkennerton/minced) (GitHub)

  miniasm:
    name: Miniasm
    link: https://github.com/lh3/miniasm
    description: Ultrafast de novo assembly for long noisy reads (though having no consensus step)
    cite: |
      Li H [Miniasm: Ultrafast de novo assembly for long noisy reads](https://github.com/lh3/miniasm) (GitHub)

  minimap2:
    name: Minimap2
    link: https://github.com/lh3/minimap2
    description: A versatile pairwise aligner for genomic and spliced nucleotide sequences
    cite: |
      Li H [Minimap2: pairwise alignment for nucleotide sequences.](https://doi.org/10.1093/bioinformatics/bty191) _Bioinformatics_ 34:3094-3100 (2018)

  mobsuite:
    name: MOB-suite
    link: https://github.com/phac-nml/mob-suite
    description: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies
    cite: |
      Robertson J, Nash JHE [MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies.](https://doi.org/10.1099/mgen.0.000206) _Microbial Genomics_ 4(8). (2018)

  mykrobe:
    name: Mykrobe
    link: https://github.com/Mykrobe-tools/mykrobe
    description: Antibiotic resistance prediction in minutes
    cite: |
      Hunt M, Bradley P, Lapierre SG, Heys S, Thomsit M, Hall MB, Malone KM, Wintringer P, Walker TM, Cirillo DM, Comas I, Farhat MR, Fowler P, Gardy J, Ismail N, Kohl TA, Mathys V, Merker M, Niemann S, Omar SV, Sintchenko V, Smith G, Supply P, Tahseen S, Wilcox M, Arandjelovic I, Peto TEA, Crook, DW, Iqbal Z [Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe](https://doi.org/10.12688/wellcomeopenres.15603.1) _Wellcome Open Research_ 4, 191. (2019)

  nanoplot:
    name: NanoPlot
    link: https://github.com/wdecoster/NanoPlot
    description: Plotting scripts for long read sequencing data
    cite: |
      De Coster W, D’Hert S, Schultz DT, Cruts M, Van Broeckhoven C [NanoPack: visualizing and processing long-read sequencing data](https://doi.org/10.1093/bioinformatics/bty149) _Bioinformatics_ Volume 34, Issue 15 (2018) 

  nanoq:
    name: Nanoq
    link: https://github.com/esteinig/nanoq
    description: Minimal but speedy quality control for nanopore reads in Rust
    cite: |
      Steinig E [Nanoq: Minimal but speedy quality control for nanopore reads in Rust](https://github.com/esteinig/nanoq) (GitHub)

  ncbigenomedownload:
    name: ncbi-genome-download
    link: https://github.com/kblin/ncbi-genome-download
    description: Scripts to download genomes from the NCBI FTP servers
    cite: |
      Blin K [ncbi-genome-download: Scripts to download genomes from the NCBI FTP servers](https://github.com/kblin/ncbi-genome-download) (GitHub)

  nextflow:
    name: Nextflow
    link: https://github.com/nextflow-io/nextflow
    description: A DSL for data-driven computational pipelines.
    cite: |
      Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C [Nextflow enables reproducible computational workflows.](https://www.nature.com/articles/nbt.3820.pdf?origin=ppub) _Nat. Biotechnol._ 35, 316–319 (2017)

  ngmaster:
    name: ngmaster
    link: https://github.com/MDU-PHL/ngmaster
    description: _In silico_ multi-antigen sequence typing for _Neisseria gonorrhoeae_ (NG-MAST)
    cite: |
      Kwong J, Gonçalves da Silva A, Schultz M, Seeman T [ngmaster - _In silico_ multi-antigen sequence typing for _Neisseria gonorrhoeae_ (NG-MAST)](https://github.com/MDU-PHL/ngmaster) (GitHub)

  nhmmer:
    name: nhmmer
    link: http://hmmer.org/
    description: DNA homology search with profile HMMs.
    cite: |
      Wheeler TJ, Eddy SR [nhmmer: DNA homology search with profile HMMs.](https://doi.org/10.1093/bioinformatics/btt403) _Bioinformatics_ 29, 2487–2489 (2013)

  panaroo:
    name: Panaroo
    link: https://github.com/gtonkinhill/panaroo
    description: An updated pipeline for pangenome investigation
    cite: |
      Tonkin-Hill G, MacAlasdair N, Ruis C, Weimann A, Horesh G, Lees JA, Gladstone RA, Lo S, Beaudoin C, Floto RA, Frost SDW, Corander J, Bentley SD, Parkhill J [Producing polished prokaryotic pangenomes with the Panaroo pipeline.](https://doi.org/10.1186/s13059-020-02090-4) _Genome Biology_ 21(1), 180. (2020)

  pasty:
    name: pasty
    link: https://github.com/rpetit3/pasty
    description: in silico serogrouping of _Pseudomonas aeruginosa_ isolates
    cite: |
      Petit III RA [pasty: in silico serogrouping of _Pseudomonas aeruginosa_ isolates](https://github.com/rpetit3/pasty) (GitHub)

  pbptyper:
    name: pbptyper
    link: https://github.com/rpetit3/pbptyper
    description: Penicillin Binding Protein (PBP) typer for _Streptococcus pneumoniae_ assemblies
    cite: |
      Petit III RA [pbptyper: In silico Penicillin Binding Protein (PBP) typer for _Streptococcus pneumoniae_ assemblies](https://github.com/rpetit3/pbptyper) (GitHub)

  phispy:
    name: PhiSpy
    link: https://github.com/linsalrob/PhiSpy
    description: Prediction of prophages from bacterial genomes
    cite: |
      Akhter S, Aziz RK, and Edwards RA [PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies.](https://doi.org/10.1093/nar/gks406) _Nucleic Acids Research_, 40(16), e126. (2012)

  phyloflash:
    name: phyloFlash
    link: https://github.com/HRGV/phyloFlash
    description: A pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset.
    cite: |
      Gruber-Vodicka HR, Seah BKB, Pruesse E [phyloFlash: Rapid Small-Subunit rRNA Profiling and Targeted Assembly from Metagenomes](https://doi.org/10.1128/mSystems.00920-20) _mSystems_ 5 (2020)

  pigz:
    name: Pigz
    link: https://zlib.net/pigz/
    description: A parallel implementation of gzip for modern multi-processor, multi-core machines.
    cite: |
      Adler M. [pigz: A parallel implementation of gzip for modern multi-processor, multi-core machines.](https://zlib.net/pigz/) _Jet Propulsion Laboratory_ (2015)

  pilon:
    name: Pilon
    link: https://github.com/broadinstitute/pilon/
    description: An automated genome assembly improvement and variant detection tool
    cite: |
      Walker BJ, Abeel T,  Shea T, Priest M, Abouelliel A, Sakthikumar S, Cuomo CA, Zeng Q, Wortman J, Young SK, Earl AM [Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement.](https://doi.org/10.1371/journal.pone.0112963) _PloS one_ 9.11 e112963 (2014)

  pirate:
    name: PIRATE
    link: http://github.com/SionBayliss/PIRATE
    description: A toolbox for pangenome analysis and threshold evaluation.
    cite: |
      Bayliss SC, Thorpe HA, Coyle NM, Sheppard SK, Feil EJ [PIRATE: A fast and scalable pangenomics toolbox for clustering diverged orthologues in bacteria.](https://doi.org/10.1093/gigascience/giz119) _Gigascience_ 8 (2019)

  plasmidfinder:
    name: PlasmidFinder
    link: https://bitbucket.org/genomicepidemiology/plasmidfinder
    description: Identifies plasmids in total or partial sequenced isolates of bacteria
    cite: |
      Carattoli A, Zankari E, García-Fernández A, Voldby Larsen M, Lund O, Villa L, Møller Aarestrup F, Hasman H [In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing.](https://doi.org/10.1128/AAC.02412-14) _Antimicrobial Agents and Chemotherapy_ 58(7), 3895–3903. (2014)

  pneumocat:
    name: PneumoCaT
    link: https://github.com/ukhsa-collaboration/PneumoCaT
    description: Pneumococcal Capsular Typing tool for NGS data
    cite: |
      Kapatai G, Sheppard CL, Al-Shahib A, Litt DJ, Underwood AP, Harrison TG, and Fry NK [Whole genome sequencing of Streptococcus pneumoniae: development, evaluation and verification of targets for serogroup and serotype prediction using an automated pipeline.](https://doi.org/10.7717/peerj.2477) PeerJ, 4, e2477. (2016)

  porechop:
    name: Porechop
    link: https://github.com/rrwick/Porechop
    description: adapter trimmer for Oxford Nanopore reads
    cite: |
      Wick RR, Judd LM, Gorrie CL, Holt KE. [Completing bacterial genome assemblies with multiplex MinION sequencing.](https://doi.org/10.1099/mgen.0.000132) _Microb Genom._ 3(10):e000132 (2017)

  pplacer:
    name: pplacer
    link: https://github.com/matsen/pplacer
    description: Phylogenetic placement and downstream analysis
    cite: |
      Matsen FA, Kodner RB, Armbrust EV [pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree.](https://doi.org/10.1186/1471-2105-11-538) _BMC Bioinformatics_ 11, 538 (2010)

  prodigal:
    name: Prodigal
    link: https://github.com/hyattpd/Prodigal
    description: Fast, reliable protein-coding gene prediction for prokaryotic genomes.
    cite: |
      Hyatt D, Chen G-L, LoCascio PF, Land ML, Larimer FW, Hauser LJ [Prodigal: prokaryotic gene recognition and translation initiation site identification.](https://doi.org/10.1186/1471-2105-11-119) _BMC Bioinformatics_ 11.1 119 (2010)

  prokka:
    name: Prokka
    link: https://github.com/tseemann/prokka
    description: Rapid prokaryotic genome annotation
    cite: |
      Seemann T [Prokka: rapid prokaryotic genome annotation](http://dx.doi.org/10.1093/bioinformatics/btu153) _Bioinformatics_ 30, 2068–2069 (2014)

  quast:
    name: QUAST
    link: http://quast.sourceforge.net/
    description: Quality Assessment Tool for Genome
    cite: |
      Gurevich A, Saveliev V, Vyahhi N, Tesler G [QUAST: quality assessment tool for genome assemblies.](http://dx.doi.org/10.1093/bioinformatics/btt086) _Bioinformatics_ 29, 1072–1075 (2013)

  racon:
    name: Racon
    link: https://github.com/lbcb-sci/racon
    description: Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads
    cite: |
      Vaser R, Sović I, Nagarajan N, Šikić M [Fast and accurate de novo genome assembly from long uncorrected reads.](http://dx.doi.org/10.1101/gr.214270.116) _Genome Res_ 27, 737–746 (2017)

  rasusa:
    name: Rasusa
    link: https://github.com/mbhall88/rasusa
    description: Randomly subsample sequencing reads to a specified coverage
    cite: |
      Hall MB [Rasusa: Randomly subsample sequencing reads to a specified coverage.](https://doi.org/10.5281/zenodo.3731394) (2019).

  raven:
    name: Raven
    link: https://github.com/lbcb-sci/raven
    description: De novo genome assembler for long uncorrected reads
    cite: |
      Vaser R, Šikić M [Time- and memory-efficient genome assembly with Raven.](https://doi.org/10.1038/s43588-021-00073-4) _Nat Comput Sci_ 1, 332–336 (2021)

  rgi:
    name: Resistance Gene Identifier (RGI)
    link: https://github.com/arpcard/rgi
    description: Software to predict resistomes from protein or nucleotide data, based on homology and SNP models.
    cite: |
      Alcock BP, Raphenya AR, Lau TTY, Tsang KK, Bouchard M, Edalatmand A, Huynh W, Nguyen A-L V, Cheng AA, Liu S, Min SY, Miroshnichenko A, Tran H-K, Werfalli RE, Nasir JA, Oloni M, Speicher DJ, Florescu A, Singh B, Faltyn M, Hernandez-Koutoucheva A, Sharma AN, Bordeleau E, Pawlowski AC, Zubyk HL, Dooley D, Griffiths E, Maguire F, Winsor GL, Beiko RG, Brinkman FSL, Hsiao WWL, Domselaar GV, McArthur AG [CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database.](https://doi.org/10.1093/nar/gkz935) _Nucleic acids research_ 48.D1, D517-D525 (2020)

  rnammer:
    name: RNAmmer
    link: http://www.cbs.dtu.dk/services/RNAmmer/
    description: Consistent and rapid annotation of ribosomal RNA genes
    cite: |
      Lagesen K, Hallin P, Rødland EA, Stærfeldt H-H, Rognes T, Ussery DW [RNAmmer: consistent annotation of rRNA genes in genomic sequences.](https://dx.doi.org/10.1093%2Fnar%2Fgkm160) _Nucleic Acids Res_ 35.9: 3100-3108 (2007)

  roary:
    name: Roary
    link: https://github.com/sanger-pathogens/Roary
    description: Rapid large-scale prokaryote pan genome analysis
    cite: |
      Page AJ, Cummins CA, Hunt M, Wong VK, Reuter S, Holden MTG, Fookes M, Falush D, Keane JA, Parkhill J [Roary: rapid large-scale prokaryote pan genome analysis.](https://doi.org/10.1093/bioinformatics/btv421) _Bioinformatics_ 31, 3691–3693 (2015)

  samclip:
    name: samclip
    link: https://github.com/tseemann/samclip
    description: Filter SAM file for soft and hard clipped alignments
    cite: |
      Seemann T [Samclip: Filter SAM file for soft and hard clipped alignments](https://github.com/tseemann/samclip) (GitHub)

  samtools:
    name: Samtools
    link: https://github.com/samtools/samtools
    description: Tools for manipulating next-generation sequencing data
    cite: |
      Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R [The Sequence Alignment/Map format and SAMtools](http://dx.doi.org/10.1093/bioinformatics/btp352). _Bioinformatics_ 25, 2078–2079 (2009)

  scoary:
    name: Scoary
    link: https://github.com/AdmiralenOla/Scoary
    description: Pan-genome wide association studies
    cite: |
      Brynildsrud O, Bohlin J, Scheffer L, Eldholm V [Rapid scoring of genes in microbial pan-genome-wide association studies with Scoary.](https://doi.org/10.1186/s13059-016-1108-8) _Genome Biol._ 17:238 (2016)

  seqsero2:
    name: SeqSero2
    link: https://github.com/denglab/SeqSero2
    description: Salmonella serotype prediction from genome sequencing data
    cite: |
      Zhang S, Den-Bakker HC, Li S, Dinsmore BA, Lane C, Lauer AC, Fields PI, Deng X. [SeqSero2: rapid and improved Salmonella serotype determination using whole genome sequencing data.](https://doi.org/10.1128/AEM.01746-19) _Appl Environ Microbiology_ 85(23):e01746-19 (2019)

  seqtk:
    name: Seqtk
    link: https://github.com/lh3/seqtk
    description: A fast and lightweight tool for processing sequences in the FASTA or FASTQ format.
    cite: |
      Li H [Toolkit for processing sequences in FASTA/Q formats](https://github.com/lh3/seqtk) (GitHub)

  seroba:
    name: Seroba
    link: https://github.com/sanger-pathogens/seroba
    description: k-mer based pipeline to identify the serotype of _Streptococcus pneumoniae_ from Illumina NGS reads
    cite: |
      Epping L, van Tonder AJ, Gladstone RA, The Global Pneumococcal Sequencing Consortium, Bentley SD, Page AJ, Keane JA [SeroBA: rapid high-throughput serotyping of Streptococcus pneumoniae from whole genome sequence data.](https://doi.org/10.1099/mgen.0.000186) _Microbial Genomics_, 4(7) (2018)

  shigatyper:
    name: ShigaTyper
    link: https://github.com/CFSAN-Biostatistics/shigatyper
    description: Shigella serotype from Illumina or Oxford Nanopore reads
    cite: |
      Wu Y, Lau HK, Lee T, Lau DK, Payne J [In Silico Serotyping Based on Whole-Genome Sequencing Improves the Accuracy of Shigella Identification.](https://doi.org/10.1128/AEM.00165-19) *Applied and Environmental Microbiology*, 85(7). (2019)

  shigeifinder:
    name: ShigEiFinder
    link: https://github.com/LanLab/ShigEiFinder
    description: Cluster informed Shigella and EIEC serotyping tool from Illumina reads and assemblies
    cite: |
      Zhang X, Payne M, Nguyen T, Kaur S, Lan R [Cluster-specific gene markers enhance Shigella and enteroinvasive Escherichia coli in silico serotyping.](https://doi.org/10.1099/mgen.0.000704) Microbial Genomics, 7(12). (2021)

  shovill:
    name: Shovill
    link: https://github.com/tseemann/shovill
    description: Faster assembly of Illumina reads
    cite: |
      Seemann T [Shovill: De novo assembly pipeline for Illumina paired reads](https://github.com/tseemann/shovill) (GitHub)

  shovill_se:
    name: Shovill-SE
    link: https://github.com/rpetit3/shovill
    description: A fork of Shovill that includes support for single end reads.
    cite: |
      Petit III RA [Shovill-SE: A fork of Shovill that includes support for single end reads.](https://github.com/rpetit3/shovill) (GitHub)

  signalp:
    name: SignalP
    link: http://www.cbs.dtu.dk/services/SignalP-4.0/
    description: SISTR (Salmonella In Silico Typing Resource) command-line tool
    cite: |
      Petersen TN, Brunak S, von Heijne G, Nielsen H [SignalP 4.0: discriminating signal peptides from transmembrane regions.](https://doi.org/10.1038/nmeth.1701) _Nature methods_ 8.10: 785 (2011)

  sistr:
    name: SISTR
    link: https://github.com/phac-nml/sistr_cmd
    description: Finds signal peptide features in CDS
    cite: |
      Yoshida CE, Kruczkiewicz P, Laing CR, Lingohr EJ, Gannon VPJ, Nash JHE, Taboada EN [The Salmonella In Silico Typing Resource (SISTR): An Open Web-Accessible Tool for Rapidly Typing and Subtyping Draft Salmonella Genome Assemblies.](https://doi.org/10.1371/journal.pone.0147101) _PloS One_, 11(1), e0147101. (2016)

  skesa:
    name: SKESA
    link: https://github.com/ncbi/SKESA
    description: Strategic Kmer Extension for Scrupulous Assemblies
    cite: |
      Souvorov A, Agarwala R, Lipman DJ [SKESA: strategic k-mer extension for scrupulous assemblies.](https://doi.org/10.1186/s13059-018-1540-z) _Genome Biology_ 19:153 (2018)

  snippy:
    name: Snippy
    link: https://github.com/tseemann/snippy
    description: Rapid haploid variant calling and core genome alignment
    cite: |
      Seemann T [Snippy: fast bacterial variant calling from NGS reads](https://github.com/tseemann/snippy) (GitHub)

  snpeff:
    name: SnpEff
    link: http://snpeff.sourceforge.net/
    description: Genomic variant annotations and functional effect prediction toolbox.
    cite: |
      Cingolani P, Platts A, Wang LL, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Douglas M [A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.](https://doi.org/10.4161/fly.19695) _Fly_ 6(2), 80-92 (2012)

  snpdists:
    name: snp-dists
    link: https://github.com/tseemann/snp-dists
    description: Pairwise SNP distance matrix from a FASTA sequence alignment
    cite: |
      Seemann T [snp-dists - Pairwise SNP distance matrix from a FASTA sequence alignment.](https://github.com/tseemann/snp-dists) (GitHub)

  snpsites:
    name: SNP-sites
    link: https://github.com/sanger-pathogens/snp-sites
    description: Rapidly extracts SNPs from a multi-FASTA alignment.
    cite: |
      Page AJ, Taylor B, Delaney AJ, Soares J, Seemann T, Keane JA, Harris SR [SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments.](https://dx.doi.org/10.1099%2Fmgen.0.000056) _Microbial Genomics_ 2.4 (2016)

  sourmash:
    name: Sourmash
    link: https://github.com/dib-lab/sourmash
    description: Compute and compare MinHash signatures for DNA data sets.
    cite: |
      Brown CT, Irber L [sourmash: a library for MinHash sketching of DNA](http://dx.doi.org/10.21105/joss.00027). _JOSS_ 1, 27 (2016)

  spades:
    name: SPAdes
    link: https://github.com/ablab/spades
    description: An assembly toolkit containing various assembly pipelines.
    cite: |
      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.](https://doi.org/10.1089/cmb.2012.0021) _Journal of computational biology_ 19.5 455-477 (2012)

  spatyper:
    name: spaTyper
    link: https://github.com/HCGB-IGTP/spaTyper
    description: Computational method for finding spa types.
    cite: |
      Sanchez-Herrero JF, and Sullivan M [spaTyper: Staphylococcal protein A (spa) characterization pipeline](http://doi.org/10.5281/zenodo.4063625). Zenodo. (2020)

  spatyper_db:
    name: spaTyper Database
    link: https://cge.cbs.dtu.dk/services/spatyper/
    description: Database used by spaTyper
    cite: |
      Harmsen D, Claus H, Witte W, Rothgänger J, Claus H, Turnwald D, and Vogel U [Typing of methicillin-resistant _Staphylococcus aureus_ in a university hospital setting using a novel software for spa-repeat determination and database management.](https://doi.org/10.1128/jcm.41.12.5442-5448.2003) _J. Clin. Microbiol._ 41:5442-5448 (2003)

  srahumanscrubber:
    name: SRA Human Scrubber
    link: https://github.com/ncbi/sra-human-scrubber
    description: An SRA tool that takes as input local fastq file from a clinical infection sample, identifies and removes any significant human read, and outputs the edited (cleaned) fastq file that can safely be used for SRA submission
    cite: |
      Katz KS, Shutov O, Lapoint R, Kimelman M, Brister JR, and O’Sullivan C [STAT: a fast, scalable, MinHash-based k-mer tool to assess Sequence Read Archive next-generation sequence submissions.](https://doi.org/10.1186/s13059-021-02490-0) _Genome Biology_, 22(1), 270 (2021)

  ssuissero:
    name: SsuisSero
    link: https://github.com/jimmyliu1326/SsuisSero
    description: Rapid _Streptococcus suis_ serotyping
    cite: |
      Lui J [SsuisSero: Rapid _Streptococcus suis_ serotyping](https://github.com/jimmyliu1326/SsuisSero) (GitHub)

  staphopiasccmec:
    name: staphopia-sccmec
    link: https://github.com/staphopia/staphopia-sccmec
    description: A standalone version of Staphopia's SCCmec typing method.
    cite: |
      Petit III RA, Read TD [_Staphylococcus aureus_ viewed from the perspective of 40,000+ genomes.](http://dx.doi.org/10.7717/peerj.5261) _PeerJ_ 6, e5261 (2018)

  stecfinder:
    name: STECFinder
    link: https://github.com/LanLab/STECFinder
    description: Clustering and Serotyping of Shigatoxin producing _E. coli_ (STEC) using genomic cluster specific markers
    cite: |
      Zhang X, Payne M, Kaur S, and Lan R [Improved Genomic Identification, Clustering, and Serotyping of Shiga Toxin-Producing Escherichia coli Using Cluster/Serotype-Specific Gene Markers.](https://doi.org/10.3389/fcimb.2021.772574) _Frontiers in Cellular and Infection Microbiology_, 11, 772574. (2021)

  tbprofiler:
    name: TBProfiler
    link: https://github.com/jodyphelan/TBProfiler
    description: Profiling tool for _Mycobacterium tuberculosis_ to detect resistance and strain type
    cite: |
      Phelan JE, O’Sullivan DM, Machado D, Ramos J, Oppong YEA, Campino S, O’Grady J, McNerney R, Hibberd ML, Viveiros M, Huggett JF, Clark TG [Integrating informatics tools and portable sequencing technology for rapid detection of resistance to anti-tuberculous drugs.](https://doi.org/10.1186/s13073-019-0650-x) _Genome Med_ 11, 41 (2019)

  trimmomatic:
    name: Trimmomatic
    link: http://www.usadellab.org/cms/index.php?page=trimmomatic
    description: A flexible read trimming tool for Illumina NGS data
    cite: |
      Bolger AM, Lohse M, Usadel B [Trimmomatic: a flexible trimmer for Illumina sequence data.](https://doi.org/10.1093/bioinformatics/btu170) _Bioinformatics_ 30.15 2114-2120 (2014)

  unicycler:
    name: Unicycler
    link: https://github.com/rrwick/Unicycler
    description: Hybrid assembly pipeline for bacterial genomes
    cite: |
      Wick RR, Judd LM, Gorrie CL, Holt KE [Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads.](http://dx.doi.org/10.1371/journal.pcbi.1005595) _PLoS Comput. Biol._ 13, e1005595 (2017)

  vcf_annotator:
    name: VCF-Annotator
    link: https://github.com/rpetit3/vcf-annotator
    description: Add biological annotations to variants in a VCF file.
    cite: |
      Petit III RA [VCF-Annotator: Add biological annotations to variants in a VCF file.](https://github.com/rpetit3/vcf-annotator) (GitHub)

  vcflib:
    name: Vcflib
    link: https://github.com/vcflib/vcflib
    description: a simple C++ library for parsing and manipulating VCF files
    cite: |
      Garrison E [Vcflib: A C++ library for parsing and manipulating VCF files](https://github.com/vcflib/vcflib) (GitHub)

  velvet:
    name: Velvet
    link: https://github.com/dzerbino/velvet
    description: Short read de novo assembler using de Bruijn graphs
    cite: |
      Zerbino DR, Birney E [Velvet: algorithms for de novo short read assembly using de Bruijn graphs.](http://www.genome.org/cgi/doi/10.1101/gr.074492.107) _Genome research_ 18.5 821-829 (2008)

  vsearch:
    name: VSEARCH
    link: https://github.com/torognes/vsearch
    description: Versatile open-source tool for metagenomics
    cite: |
      Rognes T, Flouri T, Nichols B, Quince C, Mahé F [VSEARCH: a versatile open source tool for metagenomics.](https://doi.org/10.7717/peerj.2584) _PeerJ_ 4, e2584 (2016)

  vt:
    name: vt
    link: https://github.com/atks/vt
    description: A tool set for short variant discovery in genetic sequence data.
    cite: |
      Tan A, Abecasis GR, Kang HM [Unified representation of genetic variants.](https://doi.org/10.1093/bioinformatics/btv112) _Bioinformatics_ 31(13), 2202-2204 (2015)
