ResBlaster 0.3.8

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

1. 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

2. Making your own database

Let's say you want to make your own database called owndb. All you need is a FASTA file of nucleotide sequences, say owndb.fsa(note: the fasta file must end with .fsa). Ideally the sequence IDs would have the format >GENE___ID___ACC___CATEGORY where GENE is the name of GENE, ID is the allele ID of GENE, ACC is an accession number of the sequence source, CATEGORY is the CATEGORY of this GENE belongs to.

Your final owndb.fsa should like this:

% head -n 1 owndb.fsa
>blaOXA-62___1___AY423074___Beta-lactam
ATGAATACGATAATCTCTCGCCGGTGGCGTGCCGGCCTGTGGCGGCGGCTGGTCGGCGCG
GTCGTCTTGCCCGCAACGCTCGCCGCCACCCCTGCGGCCTATGCGGCCGACGTGCCGAAA
GCCGCGTTGGGGCGCATCACCGAGCGCGCCGACTGGGGCAAGCTGTTCGCCGCGGAGGGC
GTGAAGGGCACGATCGTGGTGCTCGACGCACGCACGCAAACCTATCAGGCCTACGACGCC
GCACGTGCCGAGAAGCGCATGTCGCCGGCGTCGACCTACAAGATATTCAACAGCCTGCTG
GCGCTCGACTCCGGGGCGCTGGACAACGAACGCGCGATCATTCCCTGGGATGGCAAGCCG
CGACGCATCAAGAACTGGAACGCGGCGATGGACCTGAGGACCGCGTTTCGCGTGTCATGC
CTGCCCTGCTATCAGGTCGTCTCGCACAAGATCGGGCGCCGGTACGCGCAGGCGAAGCTG
AACGAGGTCGGGTATGGCAACCGCACCATTGGCGGCGCGCCGGACGCCTATTGGGTCGAC
GACAGTCTGCAGATTTCGGCGCGTGAGCAGGTGGACTTCGTGCAGCGTCTCGCGCGTGGC
ACGTTGCCGTTCTCTGCGCGCTCGCAGGACATCGTGCGCCAGATGTCGATCGTCGAAGCC
ACGCCGGACTATGTGCTTCACGGCAAGACGGGTTGGTTCGTCGACAAGAAGCCCGATATC
GGCTGGTGGGTAGGGTGGATCGAGCGCGACGGCAACATCACCAGCGTCGCGATCAACATC
GACATGCTGTCGGAGGCGGACGCCCCGAAACGGGCACGCATCGTGAAGGCGGTGCTGAAG
GACCTGAAGCTGATCTGA

Run following command will add owndb.fsa to blast database

% ResBlaster -updatebd owndb.fsa

3. Features under development

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
...