{"id":27302943,"url":"https://github.com/tseemann/abricate","last_synced_at":"2025-04-12T02:49:14.631Z","repository":{"id":18712855,"uuid":"21923637","full_name":"tseemann/abricate","owner":"tseemann","description":":mag_right: :pill: Mass screening of contigs for antimicrobial and virulence genes","archived":false,"fork":false,"pushed_at":"2023-12-31T08:46:49.000Z","size":16283,"stargazers_count":398,"open_issues_count":76,"forks_count":95,"subscribers_count":28,"default_branch":"master","last_synced_at":"2025-04-03T22:45:21.827Z","etag":null,"topics":["antimicrobial-resistance-genes","bioinformatics-tool","contigs","genomic-regions","virulence-genes"],"latest_commit_sha":null,"homepage":"","language":"Perl","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/tseemann.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2014-07-17T00:59:35.000Z","updated_at":"2025-04-01T09:25:08.000Z","dependencies_parsed_at":"2022-08-07T09:00:53.591Z","dependency_job_id":"417d0274-4fe9-4315-ae67-24f31ef15c1d","html_url":"https://github.com/tseemann/abricate","commit_stats":{"total_commits":242,"total_committers":3,"mean_commits":80.66666666666667,"dds":"0.045454545454545414","last_synced_commit":"955d402a23371a61bfca48f1b9e0d30ac724e6ef"},"previous_names":[],"tags_count":24,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/tseemann%2Fabricate","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/tseemann%2Fabricate/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/tseemann%2Fabricate/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/tseemann%2Fabricate/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/tseemann","download_url":"https://codeload.github.com/tseemann/abricate/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":247934810,"owners_count":21020724,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["antimicrobial-resistance-genes","bioinformatics-tool","contigs","genomic-regions","virulence-genes"],"created_at":"2025-04-12T02:49:13.990Z","updated_at":"2025-04-12T02:49:14.615Z","avatar_url":"https://github.com/tseemann.png","language":"Perl","funding_links":[],"categories":["Science and Math"],"sub_categories":["Scientific Computing"],"readme":"[![Build Status](https://travis-ci.org/tseemann/abricate.svg?branch=master)](https://travis-ci.org/tseemann/abricate) \n[![License: GPL v2](https://img.shields.io/badge/License-GPL%20v2-blue.svg)](https://www.gnu.org/licenses/old-licenses/gpl-2.0.en.html)\n![Don't judge me](https://img.shields.io/badge/Language-Perl_5-steelblue.svg)\n\n# ABRicate\n\nMass screening of contigs for antimicrobial resistance or virulence genes.\nIt comes bundled with multiple databases: \nNCBI, CARD, ARG-ANNOT, Resfinder, MEGARES, EcOH, PlasmidFinder, Ecoli_VF and\nVFDB.\n\n## Is this the right tool for me?\n\n1. It only supports contigs, not FASTQ reads\n2. It only detects acquired resistance genes, **NOT** point mutations\n3. It uses a DNA sequence database, not protein\n4. It needs BLAST+ \u003e= 2.7 and `any2fasta` to be installed\n5. It's written in Perl :camel:\n\nIf you are happy with the above, then please continue!\nOtherwise consider using\n[Ariba](https://github.com/sanger-pathogens/ariba),\n[Resfinder](https://cge.cbs.dtu.dk/services/ResFinder/),\n[RGI](https://card.mcmaster.ca/analyze/rgi),\n[SRST2](https://github.com/katholt/srst2),\n[AMRFinderPlus](https://github.com/ncbi/amr#ncbi-antimicrobial-resistance-gene-finder-amrfinderplus),\n*etc.*\n\n## Quick Start\n\n```\n% abricate 6159.fasta\nUsing database resfinder:  2130 sequences -  Mar 17, 2017\nProcessing: 6159.fna\nFound 3 genes in 6159.fna\n#FILE     SEQUENCE     START   END     STRAND GENE     COVERAGE     COVERAGE_MAP     GAPS  %COVERAGE  %IDENTITY  DATABASE  ACCESSION  PRODUCT        RESISTANCE\n6159.fna  NC_017338.1  39177   41186   +      mecA_15  1-2010/2010  ===============  0/0   100.00     100.000    ncbi      AB505628   n/a\t     FUSIDIC_ACID\n6159.fna  NC_017338.1  727191  728356  -      norA_1   1-1166/1167  ===============  0/0   99.91      92.367     ncbi      M97169     n/a            FOSFOMYCIN\n6159.fna  NC_017339.1  10150   10995   +      blaZ_32  1-846/846    ===============  0/0   100.00     100.000    ncbi      AP004832   betalactamase  BETA-LACTAM;PENICILLIN\n```\n\n## Installation\n\n### Brew\nIf you are using the [MacOS Homebrew](http://brew.sh/) or [LinuxBrew](http://brew.sh/linuxbrew/) packaging system:\n```\nbrew install brewsci/bio/abricate\nabricate --check\nabricate --list\n```\n\n### Bioconda\nIf you use [Conda](https://conda.io/docs/install/quick.html) \nfollow the instructions to add the [Bioconda channel](https://bioconda.github.io/):\n```\nconda install -c conda-forge -c bioconda -c defaults abricate\nabricate --check\nabricate --list\n```\n\n### Source\nIf you install from source, Abricate has the following package dependencies:\n* `any2fasta` for sequence file format conversion\n* BLAST+ \u003e2.7.0 for `blastn`, `makeblastdb`, `blastdbcmd`\n* Perl modules: `LWP::Simple`, `Bio::Perl`, `JSON`, `Path::Tiny`\n* `git`, `unzip`, `gzip` for updating databases\n\nMost of these are easy to install on an Ubuntu-based system:\n```\nsudo apt-get install bioperl ncbi-blast+ gzip unzip git \\\n  libjson-perl libtext-csv-perl libpath-tiny-perl liblwp-protocol-https-perl libwww-perl\ngit clone https://github.com/tseemann/abricate.git\n./abricate/bin/abricate --check\n./abricate/bin/abricate --setupdb\n./abricate/bin/abricate ./abricate/test/assembly.fa\n```\n\n## Input\n\nAbricate takes any sequence file that `any2fasta` can convert to FASTA files (eg. Genbank,\nEMBL), and they can be optionally `gzip` or `bzip2` compressed.\n```\nabricate assembly.fa \nabricate assembly.fa.gz\nabricate assembly.gbk \nabricate assembly.gbk.bz2\n```\n\nIt can take multiple files at once too:\n```\nabricate assembly.*\nabricate /mnt/ncbi/bacteria/*.gbk.gz \n```\n\nOr you can provide it a \"file of file names\" (a \"FOFN\"):\n```\n% cat test/fofn.txt\n\nassembly.fa\nassembly.fa.gz\nassembly.gbk\nassembly.gbk.bz2\n\n% abricate --fofn test/fofn.txt\n```\n\nIt does not accept raw FASTQ reads; please use\n[Ariba](https://github.com/sanger-pathogens/ariba) or\n[SRTS2](https://github.com/katholt/srst2) for that.\n\n## Output\n\nAbricate produces a tap-separated output file with the following columns:\n\nColumn | Example | Description\n-------|---------|------------\nFILE | `Ecoli.fna` | The filename this hit came from\nSEQUENCE | `contig000324` | The sequence in the filename\nSTART | `23423` | Start coordinate in the sequence\nEND | `24117` | End coordinate\nSTRAND | `+` | Strand + or -\nGENE | `tet(M)` | AMR gene name\nCOVERAGE | `1-1920/1920` | What proportion of the gene is in our sequence\nCOVERAGE_MAP | `===============` | A visual represenation of the hit. `=`=aligned, `.`=unaligned, `/`=has_gaps\nGAPS | `1/4` | Openings / gaps in subject and query - possible psuedogene?\n%COVERAGE | `100.00%` | Proportion of gene covered\n%IDENTITY | `99.95%` | Proportion of exact nucleotide matches\nDATABASE | `ncbi` | The database this sequence comes from\nACCESSION | `NC_009632:49744-50476` | The genomic source of the sequence\nPRODUCT | `aminoglycoside O-phosphotransferase APH(3')-IIIa` | Gene product (if available)\nRESISTANCE | `TETRACYCLINE;FUSIDIC_ACID` | putative antibiotic resistance phenotype, `;`-separated\n\n## Caveats\n\n* Does not find mutational resistance, only acquired genes.\n* Gap reporting incomplete\n* Sometimes two heavily overlapping genes will be reported for the same locus\n* Possible coverage calculation issues\n\n## Databases\n\nABRicate comes with some pre-downloaded databases:\n\n* [NCBI AMRFinderPlus](https://www.ncbi.nlm.nih.gov/bioproject/PRJNA313047)\n* [CARD](https://card.mcmaster.ca/)\n* [Resfinder](https://cge.cbs.dtu.dk/services/ResFinder/)\n* [ARG-ANNOT](http://en.mediterranee-infection.com/article.php?laref=283%26titre=arg-annot)\n* [MEGARES](https://megares.meglab.org/)\n* [EcOH](https://github.com/katholt/srst2/tree/master/data)\n* [PlasmidFinder](https://cge.cbs.dtu.dk/services/PlasmidFinder/)\n* [VFDB](http://www.mgc.ac.cn/VFs/)\n* [Ecoli_VF](https://github.com/phac-nml/ecoli_vf)\n\nYou can check what you have installed with the `--list` command.\nThis lists the available databases in TSV (or CSV with `--csv`) and three\ncolumns:\n```\n% abricate --list\n\nDATABASE       SEQUENCES  DBTYPE  DATE\nargannot       1749       nucl    2019-Jul-28\ncard           2241       nucl    2019-Jul-28\necoh           597        nucl    2019-Jul-28\necoli_vf       2701       nucl    2019-Jul-28\nmegares        6635       nucl    2020-Feb-20\nncbi           4324       nucl    2019-Jul-28\nplasmidfinder  263        nucl    2019-Jul-28\nresfinder      2434       nucl    2019-Jul-28\nvfdb           2597       nucl    2019-Jul-28\n```\n\nThe default database is `ncbi`.\nYou can choose a different database using the `--db` option:\n```\n% abricate --db vfdb --quiet 6159.fa\n\n6159.fna  NC_017338.1  2724620  2726149  aur      1-1530/1530     ===============  0/0    100.00     99.346     vfdb      NP_647375\tzinc metalloproteinase aureolysin\n6159.fna  NC_017338.1  2766595  2767155  icaR     1-561/561       ===============  0/0    100.00     98.930     vfdb      NP_647402\tN-acetylglucosaminyltransferase\n6159.fna  NC_017338.1  2767319  2768557  icaA     1-1239/1239     ===============  0/0    100.00     99.677     vfdb      NP_647403\tn/a\n6159.fna  NC_017338.1  2768521  2768826  icaD     1-306/306       ===============  0/0    100.00     99.020     vfdb      NP_647404\tn/a\n6159.fna  NC_017338.1  2768823  2769695  icaB     1-873/873       ===============  0/0    100.00     99.542     vfdb      NP_647405\tn/a\n6159.fna  NC_017338.1  2769682  2770734  icaC     1-1053/1053     ===============  0/0    100.00     98.955     vfdb      NP_647406\tn/a\n6159.fna  NC_017338.1  2771040  2773085  lip      1-2046/2046     ===============  0/0    100.00     98.778     vfdb      NP_647407\ttriacylglycerol lipase precursor\n```\n\n## Combining reports across samples\n\nABRicate can combine results into a simple matrix of gene presence/absence.\nAn absent gene is denoted `.` and a present gene is represented by its '%COVERAGE`.\nThis can be individual abricate reports, or a combined one.\n\n```\n# Run abricate on each .fa file\n% abricate 1.fna \u003e 1.tab\n% abricate 2.fna \u003e 2.tab\n\n# Combine\n% abricate --summary 1.tab 2.tab\n\n#FILE     NUM_FOUND  aac(6')-aph(2'')_1  aadD_1  blaZ_32  blaZ_36  erm(A)_1  mecA_15  norA_1  spc_1  tet(M)_7\n1.tab     8          100.00              100.00  .        100.00   100.00    100.00   99.91   100.00  100.00\n2.tab     3          .                   .       100.00   .        .         100.00   99.91   .       .\n```\nOr if you ran everything in a single report, it will work too.\n```\n% abricate *.fna \u003e results.tab\n% abricate --summary results.tab \u003e summary.tab\n```\n\n## Updating the databases\n\n```\n# force download of latest version\n% abricate-get_db --db ncbi --force\n\n# re-use existing download and just regenerate the database\n% abricate-get_db --db ncbi\n```\n\n## Making your own database\n\nLet's say you want to make your own database called `tinyamr`. \nAll you need is a FASTA file of nucleotide sequences, say `tinyamr.fa`.\nIdeally the sequence IDs would have the format `\u003eDB~~~ID~~~ACC~~~RESISTANCES DESC`\nwhere `DB` is `tinyamr`, `ID` is the gene name, `ACC` is an accession\nnumber of the sequence source, `RESISTANCES` is the phenotype(s) to report,\nand `DESC` can be any textual description.\n\n```\n% cd /path/to/abricate/db     # this is the --datadir default option\n% mkdir tinyamr\n% cp /path/to/tinyamr.fa sequences\n% head -n 1 sequences\n\u003etinyamr~~~GENE_ID~~~GENE_ACC~~RESISTANCES some description here\n% abricate --setupdb\n% # or just do this: makeblastdb -in sequences -title tinyamr -dbtype nucl -hash_index\n\n% abricate --list\nDATABASE  SEQUENCES  DBTYPE  DATE\ntinyamr   173        nucl    2019-Aug-28\n\n% abricate --db tinyamr screen_this.fasta\n```\n\n## Etymology\n\nThe name \"ABRicate\" was chosen as the first 3 letters are a common acronym\nfor \"Anti-Biotic Resistance\". It also has the form of an English _verb_, \nwhich suggests the tool actual taking \"action\" against the problem of antibiotic resistance.\nIt is also relatively unique in [Google](https://www.google.com.au/search?q=abricate),\nand is unlikely to receive an infamous [JABBA Award](http://www.acgt.me/blog/2014/12/1/time-for-a-new-jabba-award-for-just-another-bogus-bioinformatics-acronym).\n\n## Citation\n\nIf you publish the results of Abricate please cite both the software _and_\nthe appropriate database you used with `--db`\n\n* Seemann T, *Abricate*, **Github** `https://github.com/tseemann/abricate`\n* NCBI AMRFinderPlus - [doi: 10.1128/AAC.00483-19](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6811410)\n* CARD - [doi:10.1093/nar/gkw1004](https://www.ncbi.nlm.nih.gov/pubmed/27789705)\n* Resfinder - [doi:10.1093/jac/dks261](https://www.ncbi.nlm.nih.gov/pubmed/22782487)\n* ARG-ANNOT - [doi:10.1128/AAC.01310-13](https://www.ncbi.nlm.nih.gov/pubmed/24145532)\n* VFDB - [doi:10.1093/nar/gkv1239](https://www.ncbi.nlm.nih.gov/pubmed/26578559)\n* PlasmidFinder - [doi:10.1128/AAC.02412-14](https://www.ncbi.nlm.nih.gov/pubmed/24777092)\n* EcOH - [doi:10.1099/mgen.0.000064](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5343136/)\n* MEGARES 2.00 - [doi:10.1093/nar/gkz1010](https://academic.oup.com/nar/article/48/D1/D561/5624973)\n## Issues\n\nPlease report problems to the [Issues Page](https://github.com/tseemann/abricate/issues).\n\n## License\n\n[GPLv2](https://raw.githubusercontent.com/tseemann/abricate/master/LICENSE)\n\n## Author\n\nTorsten Seemann | [@torstenseemann](https://twitter.com/torstenseemann) | [blog](http://thegenomefactory.blogspot.com/)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftseemann%2Fabricate","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ftseemann%2Fabricate","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftseemann%2Fabricate/lists"}