https://github.com/tseemann/abricate
:mag_right: :pill: Mass screening of contigs for antimicrobial and virulence genes
https://github.com/tseemann/abricate
antimicrobial-resistance-genes bioinformatics-tool contigs genomic-regions virulence-genes
Last synced: 6 months ago
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:mag_right: :pill: Mass screening of contigs for antimicrobial and virulence genes
- Host: GitHub
- URL: https://github.com/tseemann/abricate
- Owner: tseemann
- License: gpl-2.0
- Created: 2014-07-17T00:59:35.000Z (about 11 years ago)
- Default Branch: master
- Last Pushed: 2023-12-31T08:46:49.000Z (almost 2 years ago)
- Last Synced: 2025-04-03T22:45:21.827Z (6 months ago)
- Topics: antimicrobial-resistance-genes, bioinformatics-tool, contigs, genomic-regions, virulence-genes
- Language: Perl
- Homepage:
- Size: 15.5 MB
- Stars: 398
- Watchers: 28
- Forks: 95
- Open Issues: 76
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
[](https://travis-ci.org/tseemann/abricate)
[](https://www.gnu.org/licenses/old-licenses/gpl-2.0.en.html)
# ABRicate
Mass screening of contigs for antimicrobial resistance or virulence genes.
It comes bundled with multiple databases:
NCBI, CARD, ARG-ANNOT, Resfinder, MEGARES, EcOH, PlasmidFinder, Ecoli_VF and
VFDB.
## Is this the right tool for me?
1. It only supports contigs, not FASTQ reads
2. It only detects acquired resistance genes, **NOT** point mutations
3. It uses a DNA sequence database, not protein
4. It needs BLAST+ >= 2.7 and `any2fasta` to be installed
5. It's written in Perl :camel:
If you are happy with the above, then please continue!
Otherwise consider using
[Ariba](https://github.com/sanger-pathogens/ariba),
[Resfinder](https://cge.cbs.dtu.dk/services/ResFinder/),
[RGI](https://card.mcmaster.ca/analyze/rgi),
[SRST2](https://github.com/katholt/srst2),
[AMRFinderPlus](https://github.com/ncbi/amr#ncbi-antimicrobial-resistance-gene-finder-amrfinderplus),
*etc.*
## Quick Start
```
% abricate 6159.fasta
Using database resfinder: 2130 sequences - Mar 17, 2017
Processing: 6159.fna
Found 3 genes in 6159.fna
#FILE SEQUENCE START END STRAND GENE COVERAGE COVERAGE_MAP GAPS %COVERAGE %IDENTITY DATABASE ACCESSION PRODUCT RESISTANCE
6159.fna NC_017338.1 39177 41186 + mecA_15 1-2010/2010 =============== 0/0 100.00 100.000 ncbi AB505628 n/a FUSIDIC_ACID
6159.fna NC_017338.1 727191 728356 - norA_1 1-1166/1167 =============== 0/0 99.91 92.367 ncbi M97169 n/a FOSFOMYCIN
6159.fna NC_017339.1 10150 10995 + blaZ_32 1-846/846 =============== 0/0 100.00 100.000 ncbi AP004832 betalactamase BETA-LACTAM;PENICILLIN
```
## Installation
### Brew
If you are using the [MacOS Homebrew](http://brew.sh/) or [LinuxBrew](http://brew.sh/linuxbrew/) packaging system:
```
brew install brewsci/bio/abricate
abricate --check
abricate --list
```
### Bioconda
If you use [Conda](https://conda.io/docs/install/quick.html)
follow the instructions to add the [Bioconda channel](https://bioconda.github.io/):
```
conda install -c conda-forge -c bioconda -c defaults abricate
abricate --check
abricate --list
```
### Source
If you install from source, Abricate has the following package dependencies:
* `any2fasta` for sequence file format conversion
* BLAST+ >2.7.0 for `blastn`, `makeblastdb`, `blastdbcmd`
* Perl modules: `LWP::Simple`, `Bio::Perl`, `JSON`, `Path::Tiny`
* `git`, `unzip`, `gzip` for updating databases
Most of these are easy to install on an Ubuntu-based system:
```
sudo apt-get install bioperl ncbi-blast+ gzip unzip git \
libjson-perl libtext-csv-perl libpath-tiny-perl liblwp-protocol-https-perl libwww-perl
git clone https://github.com/tseemann/abricate.git
./abricate/bin/abricate --check
./abricate/bin/abricate --setupdb
./abricate/bin/abricate ./abricate/test/assembly.fa
```
## Input
Abricate takes any sequence file that `any2fasta` can convert to FASTA files (eg. Genbank,
EMBL), and they can be optionally `gzip` or `bzip2` compressed.
```
abricate assembly.fa
abricate assembly.fa.gz
abricate assembly.gbk
abricate assembly.gbk.bz2
```
It can take multiple files at once too:
```
abricate assembly.*
abricate /mnt/ncbi/bacteria/*.gbk.gz
```
Or you can provide it a "file of file names" (a "FOFN"):
```
% cat test/fofn.txt
assembly.fa
assembly.fa.gz
assembly.gbk
assembly.gbk.bz2
% abricate --fofn test/fofn.txt
```
It does not accept raw FASTQ reads; please use
[Ariba](https://github.com/sanger-pathogens/ariba) or
[SRTS2](https://github.com/katholt/srst2) for that.
## Output
Abricate produces a tap-separated output file with the following columns:
Column | Example | Description
-------|---------|------------
FILE | `Ecoli.fna` | The filename this hit came from
SEQUENCE | `contig000324` | The sequence in the filename
START | `23423` | Start coordinate in the sequence
END | `24117` | End coordinate
STRAND | `+` | Strand + or -
GENE | `tet(M)` | AMR gene name
COVERAGE | `1-1920/1920` | What proportion of the gene is in our sequence
COVERAGE_MAP | `===============` | A visual represenation of the hit. `=`=aligned, `.`=unaligned, `/`=has_gaps
GAPS | `1/4` | Openings / gaps in subject and query - possible psuedogene?
%COVERAGE | `100.00%` | Proportion of gene covered
%IDENTITY | `99.95%` | Proportion of exact nucleotide matches
DATABASE | `ncbi` | The database this sequence comes from
ACCESSION | `NC_009632:49744-50476` | The genomic source of the sequence
PRODUCT | `aminoglycoside O-phosphotransferase APH(3')-IIIa` | Gene product (if available)
RESISTANCE | `TETRACYCLINE;FUSIDIC_ACID` | putative antibiotic resistance phenotype, `;`-separated
## Caveats
* Does not find mutational resistance, only acquired genes.
* Gap reporting incomplete
* Sometimes two heavily overlapping genes will be reported for the same locus
* Possible coverage calculation issues
## Databases
ABRicate comes with some pre-downloaded databases:
* [NCBI AMRFinderPlus](https://www.ncbi.nlm.nih.gov/bioproject/PRJNA313047)
* [CARD](https://card.mcmaster.ca/)
* [Resfinder](https://cge.cbs.dtu.dk/services/ResFinder/)
* [ARG-ANNOT](http://en.mediterranee-infection.com/article.php?laref=283%26titre=arg-annot)
* [MEGARES](https://megares.meglab.org/)
* [EcOH](https://github.com/katholt/srst2/tree/master/data)
* [PlasmidFinder](https://cge.cbs.dtu.dk/services/PlasmidFinder/)
* [VFDB](http://www.mgc.ac.cn/VFs/)
* [Ecoli_VF](https://github.com/phac-nml/ecoli_vf)
You can check what you have installed with the `--list` command.
This lists the available databases in TSV (or CSV with `--csv`) and three
columns:
```
% abricate --list
DATABASE SEQUENCES DBTYPE DATE
argannot 1749 nucl 2019-Jul-28
card 2241 nucl 2019-Jul-28
ecoh 597 nucl 2019-Jul-28
ecoli_vf 2701 nucl 2019-Jul-28
megares 6635 nucl 2020-Feb-20
ncbi 4324 nucl 2019-Jul-28
plasmidfinder 263 nucl 2019-Jul-28
resfinder 2434 nucl 2019-Jul-28
vfdb 2597 nucl 2019-Jul-28
```
The default database is `ncbi`.
You can choose a different database using the `--db` option:
```
% abricate --db vfdb --quiet 6159.fa
6159.fna NC_017338.1 2724620 2726149 aur 1-1530/1530 =============== 0/0 100.00 99.346 vfdb NP_647375 zinc metalloproteinase aureolysin
6159.fna NC_017338.1 2766595 2767155 icaR 1-561/561 =============== 0/0 100.00 98.930 vfdb NP_647402 N-acetylglucosaminyltransferase
6159.fna NC_017338.1 2767319 2768557 icaA 1-1239/1239 =============== 0/0 100.00 99.677 vfdb NP_647403 n/a
6159.fna NC_017338.1 2768521 2768826 icaD 1-306/306 =============== 0/0 100.00 99.020 vfdb NP_647404 n/a
6159.fna NC_017338.1 2768823 2769695 icaB 1-873/873 =============== 0/0 100.00 99.542 vfdb NP_647405 n/a
6159.fna NC_017338.1 2769682 2770734 icaC 1-1053/1053 =============== 0/0 100.00 98.955 vfdb NP_647406 n/a
6159.fna NC_017338.1 2771040 2773085 lip 1-2046/2046 =============== 0/0 100.00 98.778 vfdb NP_647407 triacylglycerol lipase precursor
```
## Combining reports across samples
ABRicate can combine results into a simple matrix of gene presence/absence.
An absent gene is denoted `.` and a present gene is represented by its '%COVERAGE`.
This can be individual abricate reports, or a combined one.
```
# Run abricate on each .fa file
% abricate 1.fna > 1.tab
% abricate 2.fna > 2.tab
# Combine
% abricate --summary 1.tab 2.tab
#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
1.tab 8 100.00 100.00 . 100.00 100.00 100.00 99.91 100.00 100.00
2.tab 3 . . 100.00 . . 100.00 99.91 . .
```
Or if you ran everything in a single report, it will work too.
```
% abricate *.fna > results.tab
% abricate --summary results.tab > summary.tab
```
## Updating the databases
```
# force download of latest version
% abricate-get_db --db ncbi --force
# re-use existing download and just regenerate the database
% abricate-get_db --db ncbi
```
## Making your own database
Let's say you want to make your own database called `tinyamr`.
All you need is a FASTA file of nucleotide sequences, say `tinyamr.fa`.
Ideally the sequence IDs would have the format `>DB~~~ID~~~ACC~~~RESISTANCES DESC`
where `DB` is `tinyamr`, `ID` is the gene name, `ACC` is an accession
number of the sequence source, `RESISTANCES` is the phenotype(s) to report,
and `DESC` can be any textual description.
```
% cd /path/to/abricate/db # this is the --datadir default option
% mkdir tinyamr
% cp /path/to/tinyamr.fa sequences
% head -n 1 sequences
>tinyamr~~~GENE_ID~~~GENE_ACC~~RESISTANCES some description here
% abricate --setupdb
% # or just do this: makeblastdb -in sequences -title tinyamr -dbtype nucl -hash_index
% abricate --list
DATABASE SEQUENCES DBTYPE DATE
tinyamr 173 nucl 2019-Aug-28
% abricate --db tinyamr screen_this.fasta
```
## Etymology
The name "ABRicate" was chosen as the first 3 letters are a common acronym
for "Anti-Biotic Resistance". It also has the form of an English _verb_,
which suggests the tool actual taking "action" against the problem of antibiotic resistance.
It is also relatively unique in [Google](https://www.google.com.au/search?q=abricate),
and 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).
## Citation
If you publish the results of Abricate please cite both the software _and_
the appropriate database you used with `--db`
* Seemann T, *Abricate*, **Github** `https://github.com/tseemann/abricate`
* NCBI AMRFinderPlus - [doi: 10.1128/AAC.00483-19](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6811410)
* CARD - [doi:10.1093/nar/gkw1004](https://www.ncbi.nlm.nih.gov/pubmed/27789705)
* Resfinder - [doi:10.1093/jac/dks261](https://www.ncbi.nlm.nih.gov/pubmed/22782487)
* ARG-ANNOT - [doi:10.1128/AAC.01310-13](https://www.ncbi.nlm.nih.gov/pubmed/24145532)
* VFDB - [doi:10.1093/nar/gkv1239](https://www.ncbi.nlm.nih.gov/pubmed/26578559)
* PlasmidFinder - [doi:10.1128/AAC.02412-14](https://www.ncbi.nlm.nih.gov/pubmed/24777092)
* EcOH - [doi:10.1099/mgen.0.000064](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5343136/)
* MEGARES 2.00 - [doi:10.1093/nar/gkz1010](https://academic.oup.com/nar/article/48/D1/D561/5624973)
## Issues
Please report problems to the [Issues Page](https://github.com/tseemann/abricate/issues).
## License
[GPLv2](https://raw.githubusercontent.com/tseemann/abricate/master/LICENSE)
## Author
Torsten Seemann | [@torstenseemann](https://twitter.com/torstenseemann) | [blog](http://thegenomefactory.blogspot.com/)