find antimcirobial resistance genes on genomes
Project description
ResBlaster
____ ____ _ _
| _ \ ___ ___| __ )| | __ _ ___| |_ ___ _ __
| |_) / _ \/ __| _ \| |/ _` / __| __/ _ \ '__|
| _ < __/\__ \ |_) | | (_| \__ \ || __/ |
|_| \_\___||___/____/|_|\__,_|___/\__\___|_|
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
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
ResBlaster-0.3.7.tar.gz
(12.6 MB
view hashes)
Built Distribution
ResBlaster-0.3.7-py3-none-any.whl
(13.9 MB
view hashes)
Close
Hashes for ResBlaster-0.3.7-py3-none-any.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | de4e17f66276cfc46dd4a35e532d901dfc166945c0608f3b2e5723c6576004e1 |
|
MD5 | 1e2e7a21e13e201bbf69a96d69bd5284 |
|
BLAKE2b-256 | 76c147b146e100818d60e8a2cf3f430aa583d2db6817c5b72dc1d4c72ce5a628 |