Package Recipe 'rgi'

recipe rgi

This tool provides a preliminary annotation of your DNA sequence(s) based upon the data available in The Comprehensive Antibiotic Resistance Database (CARD). Hits to genes tagged with Antibiotic Resistance ontology terms will be highlighted. As CARD expands to include more pathogens, genomes, plasmids, and ontology terms this tool will grow increasingly powerful in providing first-pass detection of antibiotic resistance associated genes. See license at CARD website

Homepage:: https://card.mcmaster.ca
License:: https://card.mcmaster.ca/about
Recipe:: /rgi/meta.yaml
Links:: doi: 10.1093/nar/gkz935

package rgi¶

Versions:

6.0.2-0, 6.0.1-1, 6.0.1-0, 6.0.0-0, 5.2.1-2, 5.2.1-1, 5.2.1-0, 5.2.0-0, 5.1.1-0,

6.0.2-0, 6.0.1-1, 6.0.1-0, 6.0.0-0, 5.2.1-2, 5.2.1-1, 5.2.1-0, 5.2.0-0, 5.1.1-0, 5.1.0-1, 5.1.0-0, 5.0.0-0, 4.2.2-1, 4.2.2-0, 4.0.3-3, 4.0.3-2, 4.0.3-1, 4.0.3-0, 3.2.1-4, 3.2.1-3, 3.2.1-2, 3.2.1-1, 3.2.0-3, 3.2.0-2, 3.2.0-1, 3.1.2-3, 3.1.2-2, 3.1.2-1, 3.1.1-2, 3.1.1-1, 3.1.0-1, 3.1.0-0

Depends:

bamtools >=2.5.1,<2.5.2.0a0
beautifulsoup4 4.9.3
bedtools >=2.28.0
biopython 1.78.*
blast 2.9.0.*
bowtie2 >=2.3.4.3
bwa >=0.7.17
dask
diamond 0.8.36.*
filetype >=1.0.0
kma >=1.2.26
lxml 4.6.5
matplotlib-base >=2.1.2
oligoarrayaux 3.8.*
pandas >=0.15.0
prodigal 2.6.3.*
pyahocorasick >=1.1.7
pyfaidx >=0.5.4.1
pyrodigal >=2.0.0
pysam 0.16.0.1
python >=3.5
requests 2.24.0
samtools 1.9.*
seaborn >=0.8.1
six >=1.7.0
wget
zlib >=1.2.13,<1.3.0a0

Required By:

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install rgi

and update with:

conda update rgi

or use the docker container:

docker pull quay.io/biocontainers/rgi:<tag>

(see rgi/tags for valid values for <tag>)

Download stats¶

Link to this page¶

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/rgi/README.html)