find antimcirobial resistance genes on genomes
Project description
ResBlaster
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Installation
pip3 install ResBlaster
Dependency
- BLAST+ >2.7.0
- cvmblaster (v0.3.8)
you should add BLAST in your PATH
Blast installation
Windows
Following this tutorial: Add blast into your windows PATH
Linux/Mac
The easyest way to install blast is:
conda install -c bioconda blast
Usage
Initialize reference database
After finish installation, you should first initialize the reference database using following command
ResBlaster -init
Usage: ResBlaster -i <genome assemble directory> -db <reference database> -o <output_directory> -minid 90 -mincov 60 -t 4
optional arguments:
-h, --help show this help message and exit
-i I <input_path>: the PATH to the directory of assembled genome files
-o O <output_directory>: output PATH
-db DB <database>: resfinder or others, You colud check database list using -list parameter
-minid MINID <minimum threshold of identity>, default=90
-mincov MINCOV <minimum threshold of coverage>, default=60
-list <show database list>
-init <initialize the reference database>
-t T <number of threads>: default=8
-store_arg_seq save the nucleotide and amino acid sequence of find genes on genome
-v, --version Display version
Following database are currently under development and will be available soon:
Database | Description |
---|---|
vfdb_core | The core dataset of vfdb |
vfdb_full | The full database of vfdb |
ncbi | Bacterial Antimicrobial Resistance Reference Gene Database from NCBI |
resfinder | ARGs from ResFinder |
ssuis_sero | The serotype database for Streptococcus suis |
hps | The serotype database for Haemophilus parasuis |
lmo | Listeria monocytogenes relevant genes from Pasteur Institute |
... |
Project details
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