resblaster 0.3.6

find antimcirobial resistance genes on genomes

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
...