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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)