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Acknowledgements

Bactopia is truly a case of "standing upon the shoulders of giants". Bactopia currently includes more than 132 datasets and software packages. Nearly every component uses, from the workflow, datasets, software packages, even the framework for this site, was created by others and made freely available to the public.

I would like to personally extend my many thanks and gratitude to the authors of these software packages and public datasets. If you've made it this far, I owe you a beer 🍻 (or coffee ☕!) if we ever encounter one another in person. Really, thank you very much!

Please Cite Datasets and Tools

If you have used Bactopia in your work, please be sure to cite any datasets or software you may have used.

Influences

nf-core

nf-core is group of great individuals volunteering their time to create a set of curated Nextflow analysis pipelines. The nf-core Team is putting together some amazing practices that I think really strengthen the Nextflow community as a whole!

Since the beginning I have always had the idea of Bactopia one day being apart of nf-core. Unfortunately, I think Bactopia is a much to big at this point to fit the nf-core mold, but that's OK! There are still many nf-core practices I've been able to adapt into Bactopia.

  1. Arguement parsing based on nf-core library
  2. All Bactopia Tools are adapted from nf-core/modules
  3. Testing implemented to follow nf-core/modules

By implementing these practices, Bactopia I believe is much better pipeline to use. For this I'm very grateful to the nf-core community! Thank you!

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. Nat Biotechnol. (2020)

Public Datasets

Below is a list of 19 public datasets that could have potentially been included during the Build Datasets step.

Ariba Reference Datasets

These datasets are available using Ariba's getref function. You can learn more about this function at Ariba's Wiki.

  1. ARG-ANNOT
    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. Antimicrob. Agents Chemother 58, 212–220 (2014)

  2. CARD
    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. Nucleic acids research 48.D1, D517-D525 (2020)

  3. EcOH
    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. Microbial Genomics, 2(7), e000064. (2016)

  4. MEGARes
    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. Nucleic Acids Res. 45, D574–D580 (2017)

  5. MEGARes 2.0
    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. Nucleic Acids Research, 48(D1), D561–D569. (2020)

  6. NCBI Reference Gene Catalog
    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. Antimicrob. Agents Chemother. (2019)

  7. PlasmidFinder
    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. Antimicrob. Agents Chemother. 58, 3895–3903 (2014)

  8. ResFinder
    Zankari E, Hasman H, Cosentino S, Vestergaard M, Rasmussen S, Lund O, Aarestrup FM, Larsen MV Identification of acquired antimicrobial resistance genes. J. Antimicrob. Chemother. 67, 2640–2644 (2012)

  9. SRST2
    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. Genome Med. 6, 90 (2014)

  10. VFDB
    Chen L, Zheng D, Liu B, Yang J, Jin Q VFDB 2016: hierarchical and refined dataset for big data analysis--10 years on. Nucleic Acids Res. 44, D694–7 (2016)

  11. VirulenceFinder
    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. J. Clin. Microbiol. 52, 1501–1510 (2014)

Minmer Datasets

  1. Mash Refseq (release 88) Sketch
    Ondov BD, Starrett GJ, Sappington A, Kostic A, Koren S, Buck CB, Phillippy AM Mash Screen: high-throughput sequence containment estimation for genome discovery Genome Biol 20, 232 (2019)

  2. Sourmash Genbank LCA Signature
    Brown CT, Irber L sourmash: a library for MinHash sketching of DNA. JOSS 1, 27 (2016)

Everything Else

  1. eggNOG 5.0 Database
    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. Nucleic Acids Res. 47, D309–D314 (2019)

  2. Genome Taxonomy Database
    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 Nucleic Acids Research gkab776 (2021)

  3. MOB-suite Database
    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. Microbial Genomics, 6(10)(2020)

  4. NCBI RefSeq Database
    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. Nucleic Acids Res. 44, D733–45 (2016)

  5. PubMLST.org
    Jolley KA, Bray JE, Maiden MCJ Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications. Wellcome Open Res 3, 124 (2018)

  6. SILVA rRNA Database
    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. Nucleic Acids Res. 41, D590–6 (2013)

Software Included In Bactopia

Below are 113 of software packages used (directly and indirectly) by Bactopia. A link to the software page as well as the citation (if available) have been included.

  1. Abricate
    Mass screening of contigs for antimicrobial and virulence genes
    Seemann T Abricate: mass screening of contigs for antimicrobial and virulence genes (GitHub)

  2. AgrVATE
    Rapid identification of Staphylococcus aureus agr locus type and agr operon variants.
    Raghuram V. AgrVATE: Rapid identification of Staphylococcus aureus agr locus type and agr operon variants. (GitHub)

  3. AMRFinderPlus
    Find acquired antimicrobial resistance genes and some point mutations in protein or assembled nucleotide sequences.
    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. Antimicrob. Agents Chemother. (2019)

  4. any2fasta
    Convert various sequence formats to FASTA
    Seemann T any2fasta: Convert various sequence formats to FASTA (GitHub)

  5. Aragorn
    Finds transfer RNA features (tRNA)
    Laslett D, Canback B ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Res. 32(1):11-6 (2004)

  6. Ariba
    Antimicrobial Resistance Identification By Assembly
    Hunt M, Mather AE, Sánchez-Busó L, Page AJ, Parkhill J, Keane JA, Harris SR ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads. Microb Genom 3, e000131 (2017)

  7. ART
    A set of simulation tools to generate synthetic next-generation sequencing reads
    Huang W, Li L, Myers JR, Marth GT ART: a next-generation sequencing read simulator. Bioinformatics 28, 593–594 (2012)

  8. assembly-scan
    Generate basic stats for an assembly.
    Petit III RA assembly-scan: generate basic stats for an assembly (GitHub)

  9. Bakta
    Rapid & standardized annotation of bacterial genomes & plasmids
    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. Microbial Genomics 7(11) (2021)

  10. Barrnap
    Bacterial ribosomal RNA predictor
    Seemann T Barrnap: Bacterial ribosomal RNA predictor (GitHub)

  11. BBTools
    BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data.
    Bushnell B BBMap short read aligner, and other bioinformatic tools. (Link)

  12. BCFtools
    Utilities for variant calling and manipulating VCFs and BCFs.
    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 GigaScience Volume 10, Issue 2 (2021)

  13. Bedtools
    A powerful toolset for genome arithmetic.
    Quinlan AR, Hall IM BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841–842 (2010)

  14. BLAST
    Basic Local Alignment Search Tool
    Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL BLAST+: architecture and applications. BMC Bioinformatics 10, 421 (2009)

  15. Bowtie2
    A fast and sensitive gapped read aligner
    Langmead B, Salzberg SL Fast gapped-read alignment with Bowtie 2. Nat. Methods. 9, 357–359 (2012)

  16. BWA
    Burrow-Wheeler Aligner for short-read alignment
    Li H Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv [q-bio.GN] (2013)

  17. CD-HIT
    Accelerated for clustering the next-generation sequencing data
    Li W, Godzik A Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22, 1658–1659 (2006)

  18. CD-HIT-EST
    Accelerated for clustering the next-generation sequencing data
    Fu L, Niu B, Zhu Z, Wu S, Li W CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics 28, 3150–3152 (2012)

  19. CheckM
    Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes
    Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 25, 1043–1055 (2015)

  20. ClonalFramML
    Efficient Inference of Recombination in Whole Bacterial Genomes
    Didelot X, Wilson DJ ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes. PLoS Comput Biol 11(2) e1004041 (2015)

  21. DIAMOND
    Accelerated BLAST compatible local sequence aligner.
    Buchfink B, Xie C, Huson DH Fast and sensitive protein alignment using DIAMOND. Nat. Methods. 12, 59–60 (2015)

  22. ECTyper
    In-silico prediction of Escherichia coli serotype
    Laing C, Bessonov K, Sung S, La Rose C ECTyper - In silico prediction of Escherichia coli serotype (GitHub)

  23. eggNOG-mapper
    Fast genome-wide functional annotation through orthology assignment
    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. Mol. Biol. Evol. 34, 2115–2122 (2017)

  24. emmtyper
    emm Automatic Isolate Labeller
    Tan A, Seemann T, Lacey D, Davies M, Mcintyre L, Frost H, Williamson D, Gonçalves da Silva A emmtyper - emm Automatic Isolate Labeller (GitHub)

  25. FastANI
    Fast Whole-Genome Similarity (ANI) Estimation
    Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat. Commun. 9, 5114 (2018)

  26. FastQC
    A quality control analysis tool for high throughput sequencing data.
    Andrews S FastQC: a quality control tool for high throughput sequence data. (WebLink)

  27. fastq-dl
    Download FASTQ files from SRA or ENA repositories.
    Petit III RA fastq-dl: Download FASTQ files from SRA or ENA repositories. (GitHub)

  28. fastq-scan
    Output FASTQ summary statistics in JSON format
    Petit III RA fastq-scan: generate summary statistics of input FASTQ sequences. (GitHub)

  29. FastTree
    Approximately-maximum-likelihood phylogenetic trees
    Price MN, Dehal PS, Arkin AP FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments. PLoS One 5, e9490 (2010)

  30. FLASH
    A fast and accurate tool to merge paired-end reads.
    Magoč T, Salzberg SL FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27.21 2957-2963 (2011)

  31. Flye
    De novo assembler for single molecule sequencing reads using repeat graphs
    Kolmogorov M, Yuan J, Lin Y, Pevzner P Assembly of Long Error-Prone Reads Using Repeat Graphs Nature Biotechnology (2019)

  32. freebayes
    Bayesian haplotype-based genetic polymorphism discovery and genotyping
    Garrison E, Marth G Haplotype-based variant detection from short-read sequencing. arXiv preprint arXiv:1207.3907 [q-bio.GN] (2012)

  33. GAMMA
    Gene Allele Mutation Microbial Assessment
    Stanton RA, Vlachos N, Halpin AL GAMMA: a tool for the rapid identification, classification, and annotation of translated gene matches from sequencing data. Bioinformatics (2021)

  34. GNU Parallel
    A shell tool for executing jobs in parallel
    Tange O GNU Parallel (2018)

  35. GTDB-Tk
    A toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes
    Chaumeil PA, Mussig AJ, Hugenholtz P, Parks DH GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. Bioinformatics (2019)

  36. hicap
    in silico typing of the H. influenzae cap locus
    Watts SC, Holt KE hicap: in silico serotyping of the Haemophilus influenzae capsule locus. Journal of Clinical Microbiology JCM.00190-19 (2019)

  37. HMMER
    Biosequence analysis using profile hidden Markov models
    Eddy SR Accelerated Profile HMM Searches. PLoS Comput. Biol. 7, e1002195 (2011)

  38. HpsuisSero
    Rapid Haemophilus parasuis serotyping
    Lui J HpsuisSero: Rapid Haemophilus parasuis serotyping (GitHub)

  39. Infernal
    Searches DNA sequence databases for RNA structure and sequence similarities
    Nawrocki EP, Eddy SR Infernal 1.1: 100-fold faster RNA homology searches. Bioinformatics 29(22), 2933-2935 (2013)

  40. IQ-TREE
    Efficient phylogenomic software by maximum likelihood
    Nguyen L-T, Schmidt HA, von Haeseler A, Minh BQ IQ-TREE: A fast and effective stochastic algorithm for estimating maximum likelihood phylogenies. Mol. Biol. Evol. 32:268-274 (2015)

  41. ModelFinder
    Used for automatic model selection
    Kalyaanamoorthy S, Minh BQ, Wong TKF, von Haeseler A, Jermiin LS ModelFinder - Fast model selection for accurate phylogenetic estimates. Nat. Methods 14:587-589 (2017)

  42. UFBoot2
    Used to conduct ultrafast bootstrapping
    Hoang DT, Chernomor O, von Haeseler A, Minh BQ, Vinh LS UFBoot2: Improving the ultrafast bootstrap approximation. Mol. Biol. Evol. 35:518–522 (2018)

  43. ISMapper
    IS mapping software
    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. BMC Genomics 16, 667 (2015)

  44. Kaptive
    Surface polysaccharide loci for Klebsiella pneumoniae species complex and Acinetobacter baumannii genomes
    Wyres KL, Wick RR, Gorrie C, Jenney A, Follador R, Thomson NR, Holt KE Identification of Klebsiella capsule synthesis loci from whole genome data. Microbial genomics 2(12) (2016)

  45. Kleborate
    Genotyping tool for Klebsiella pneumoniae and its related species complex
    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. Nat Commun 12, 4188 (2021)

  46. KMC
    Fast and frugal disk based k-mer counter
    Deorowicz S, Kokot M, Grabowski Sz, Debudaj-Grabysz A KMC 2: Fast and resource-frugal k-mer counting Bioinformatics 31(10):1569–1576 (2015)

  47. Kraken2

Wood DE, Lu J, Langmead B Improved metagenomic analysis with Kraken 2. Genome Biology, 20(1), 257. (2019)

  1. legsta
    In silico Legionella pneumophila Sequence Based Typing
    Seemann T legsta: In silico Legionella pneumophila Sequence Based Typing (GitHub)

  2. Lighter
    Fast and memory-efficient sequencing error corrector
    Song L, Florea L, Langmead B Lighter: Fast and Memory-efficient Sequencing Error Correction without Counting. Genome Biol. 15(11):509 (2014)

  3. LisSero
    In silico serotype prediction for Listeria monocytogenes
    Kwong J, Zhang J, Seeman T, Horan, K, Gonçalves da Silva A LisSero - In silico serotype prediction for Listeria monocytogenes (GitHub)

  4. MAFFT
    Multiple alignment program for amino acid or nucleotide sequences
    Katoh K, Standley DM MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 772–780 (2013)

  5. Mash
    Fast genome and metagenome distance estimation using MinHash
    Ondov BD, Treangen TJ, Melsted P, Mallonee AB, Bergman NH, Koren S, Phillippy AM Mash: fast genome and metagenome distance estimation using MinHash. Genome Biol 17, 132 (2016)

  6. Mash
    High-throughput sequence containment estimation
    Ondov BD, Starrett GJ, Sappington A, Kostic A, Koren S, Buck CB, Phillippy AM Mash Screen: high-throughput sequence containment estimation for genome discovery Genome Biol 20, 232 (2019)

  7. Mashtree
    Create a tree using Mash distances
    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. Journal of Open Source Software, 4(44), 1762 (2019)

  8. maskrc-svg
    Masks recombination as detected by ClonalFrameML or Gubbins
    Kwong J maskrc-svg - Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG. (GitHub)

  9. McCortex
    De novo genome assembly and multisample variant calling
    Turner I, Garimella KV, Iqbal Z, McVean G Integrating long-range connectivity information into de Bruijn graphs. Bioinformatics 34, 2556–2565 (2018)

  10. Medaka
    Sequence correction provided by ONT Research
    ONT Research Medaka: Sequence correction provided by ONT Research (GitHub)

  11. meningotype
    In silico serotyping, finetyping and Bexsero antigen sequence typing of Neisseria meningitidis
    Kwong JC, Gonçalves da Silva A, Stinear TP, Howden BP, & Seemann T meningotype: in silico typing for Neisseria meningitidis. (GitHub)

  12. MEGAHIT
    Ultra-fast and memory-efficient (meta-)genome assembler
    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. Bioinformatics 31.10 1674-1676 (2015)

  13. mlst
    Scan contig files against PubMLST typing schemes
    Seemann T mlst: scan contig files against PubMLST typing schemes (GitHub)

  14. MinCED
    Mining CRISPRs in Environmental Datasets
    Skennerton C MinCED: Mining CRISPRs in Environmental Datasets (GitHub)

  15. Miniasm
    Ultrafast de novo assembly for long noisy reads (though having no consensus step)
    Li H Miniasm: Ultrafast de novo assembly for long noisy reads (GitHub)

  16. Minimap2
    A versatile pairwise aligner for genomic and spliced nucleotide sequences
    Li H Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34:3094-3100 (2018)

  17. MOB-suite
    Software tools for clustering, reconstruction and typing of plasmids from draft assemblies
    Robertson J, Nash JHE MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies. Microbial Genomics 4(8). (2018)

  18. NanoPlot
    Plotting scripts for long read sequencing data
    De Coster W, D’Hert S, Schultz DT, Cruts M, Van Broeckhoven C NanoPack: visualizing and processing long-read sequencing data Bioinformatics Volume 34, Issue 15 (2018)

  19. Nanoq
    Minimal but speedy quality control for nanopore reads in Rust
    Steinig E Nanoq: Minimal but speedy quality control for nanopore reads in Rust (GitHub)

  20. ncbi-genome-download
    Scripts to download genomes from the NCBI FTP servers
    Blin K ncbi-genome-download: Scripts to download genomes from the NCBI FTP servers (GitHub)

  21. Nextflow
    A DSL for data-driven computational pipelines.
    Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C Nextflow enables reproducible computational workflows. Nat. Biotechnol. 35, 316–319 (2017)

  22. ngmaster
    In silico multi-antigen sequence typing for Neisseria gonorrhoeae (NG-MAST)
    Kwong J, Gonçalves da Silva A, Schultz M, Seeman T ngmaster - In silico multi-antigen sequence typing for Neisseria gonorrhoeae (NG-MAST) (GitHub)

  23. nhmmer
    DNA homology search with profile HMMs.
    Wheeler TJ, Eddy SR nhmmer: DNA homology search with profile HMMs. Bioinformatics 29, 2487–2489 (2013)

  24. phyloFlash
    A pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset.
    Gruber-Vodicka HR, Seah BKB, Pruesse E phyloFlash: Rapid Small-Subunit rRNA Profiling and Targeted Assembly from Metagenomes mSystems 5 (2020)

  25. Pigz
    A parallel implementation of gzip for modern multi-processor, multi-core machines.
    Adler M. pigz: A parallel implementation of gzip for modern multi-processor, multi-core machines. Jet Propulsion Laboratory (2015)

  26. Pilon
    An automated genome assembly improvement and variant detection tool
    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. PloS one 9.11 e112963 (2014)

  27. PIRATE
    A toolbox for pangenome analysis and threshold evaluation.
    Bayliss SC, Thorpe HA, Coyle NM, Sheppard SK, Feil EJ PIRATE: A fast and scalable pangenomics toolbox for clustering diverged orthologues in bacteria. Gigascience 8 (2019)

  28. Porechop
    adapter trimmer for Oxford Nanopore reads
    Wick RR, Judd LM, Gorrie CL, Holt KE. Completing bacterial genome assemblies with multiplex MinION sequencing. Microb Genom. 3(10):e000132 (2017)

  29. pplacer
    Phylogenetic placement and downstream analysis
    Matsen FA, Kodner RB, Armbrust EV pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree. BMC Bioinformatics 11, 538 (2010)

  30. Prodigal
    Fast, reliable protein-coding gene prediction for prokaryotic genomes.
    Hyatt D, Chen G-L, LoCascio PF, Land ML, Larimer FW, Hauser LJ Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11.1 119 (2010)

  31. Prokka
    Rapid prokaryotic genome annotation
    Seemann T Prokka: rapid prokaryotic genome annotation Bioinformatics 30, 2068–2069 (2014)

  32. QUAST
    Quality Assessment Tool for Genome
    Gurevich A, Saveliev V, Vyahhi N, Tesler G QUAST: quality assessment tool for genome assemblies. Bioinformatics 29, 1072–1075 (2013)

  33. Racon
    Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads
    Vaser R, Sović I, Nagarajan N, Šikić M Fast and accurate de novo genome assembly from long uncorrected reads. Genome Res 27, 737–746 (2017)

  34. Rasusa
    Randomly subsample sequencing reads to a specified coverage
    Hall MB Rasusa: Randomly subsample sequencing reads to a specified coverage. (2019).

  35. Raven
    De novo genome assembler for long uncorrected reads
    Vaser R, Šikić M Time- and memory-efficient genome assembly with Raven. Nat Comput Sci 1, 332–336 (2021)

  36. Resistance Gene Identifier (RGI)
    Software to predict resistomes from protein or nucleotide data, based on homology and SNP models.
    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. Nucleic acids research 48.D1, D517-D525 (2020)

  37. RNAmmer
    Consistent and rapid annotation of ribosomal RNA genes
    Lagesen K, Hallin P, Rødland EA, Stærfeldt H-H, Rognes T, Ussery DW RNAmmer: consistent annotation of rRNA genes in genomic sequences. Nucleic Acids Res 35.9: 3100-3108 (2007)

  38. Roary
    Rapid large-scale prokaryote pan genome analysis
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    Filter SAM file for soft and hard clipped alignments
    Seemann T Samclip: Filter SAM file for soft and hard clipped alignments (GitHub)

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    Tools for manipulating next-generation sequencing data
    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. Bioinformatics 25, 2078–2079 (2009)

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    Pan-genome wide association studies
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    Salmonella serotype prediction from genome sequencing data
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  43. Seqtk
    A fast and lightweight tool for processing sequences in the FASTA or FASTQ format.
    Li H Toolkit for processing sequences in FASTA/Q formats (GitHub)

  44. ShigaTyper
    Shigella serotype from Illumina or Oxford Nanopore reads
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  45. Shovill
    Faster assembly of Illumina reads
    Seemann T Shovill: De novo assembly pipeline for Illumina paired reads (GitHub)

  46. SignalP
    SISTR (Salmonella In Silico Typing Resource) command-line tool
    Petersen TN, Brunak S, von Heijne G, Nielsen H SignalP 4.0: discriminating signal peptides from transmembrane regions. Nature methods 8.10: 785 (2011)

  47. SISTR
    Finds signal peptide features in CDS
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    Strategic Kmer Extension for Scrupulous Assemblies
    Souvorov A, Agarwala R, Lipman DJ SKESA: strategic k-mer extension for scrupulous assemblies. Genome Biology 19:153 (2018)

  49. Snippy
    Rapid haploid variant calling and core genome alignment
    Seemann T Snippy: fast bacterial variant calling from NGS reads (GitHub)

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    Genomic variant annotations and functional effect prediction toolbox.
    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. Fly 6(2), 80-92 (2012)

  51. snp-dists
    Pairwise SNP distance matrix from a FASTA sequence alignment
    Seemann T snp-dists - Pairwise SNP distance matrix from a FASTA sequence alignment. (GitHub)

  52. SNP-sites
    Rapidly extracts SNPs from a multi-FASTA alignment.
    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. Microbial Genomics 2.4 (2016)

  53. Sourmash
    Compute and compare MinHash signatures for DNA data sets.
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  54. SPAdes
    An assembly toolkit containing various assembly pipelines.
    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. Journal of computational biology 19.5 455-477 (2012)

  55. spaTyper
    Computational method for finding spa types.
    Sanchez-Herrero JF, and Sullivan M spaTyper: Staphylococcal protein A (spa) characterization pipeline. Zenodo. (2020)

  56. spaTyper Database
    Database used by spaTyper
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  57. SsuisSero
    Rapid Streptococcus suis serotyping
    Lui J SsuisSero: Rapid Streptococcus suis serotyping (GitHub)

  58. staphopia-sccmec
    A standalone version of Staphopia's SCCmec typing method.
    Petit III RA, Read TD Staphylococcus aureus viewed from the perspective of 40,000+ genomes. PeerJ 6, e5261 (2018)

  59. TBProfiler
    Profiling tool for Mycobacterium tuberculosis to detect resistance and strain type
    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. Genome Med 11, 41 (2019)

  60. Trimmomatic
    A flexible read trimming tool for Illumina NGS data
    Bolger AM, Lohse M, Usadel B Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30.15 2114-2120 (2014)

  61. Unicycler
    Hybrid assembly pipeline for bacterial genomes
    Wick RR, Judd LM, Gorrie CL, Holt KE Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput. Biol. 13, e1005595 (2017)

  62. VCF-Annotator
    Add biological annotations to variants in a VCF file.
    Petit III RA VCF-Annotator: Add biological annotations to variants in a VCF file. (GitHub)

  63. Vcflib
    a simple C++ library for parsing and manipulating VCF files
    Garrison E Vcflib: A C++ library for parsing and manipulating VCF files (GitHub)

  64. Velvet
    Short read de novo assembler using de Bruijn graphs
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  65. VSEARCH
    Versatile open-source tool for metagenomics
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  66. vt
    A tool set for short variant discovery in genetic sequence data.
    Tan A, Abecasis GR, Kang HM Unified representation of genetic variants. Bioinformatics 31(13), 2202-2204 (2015)