ResBlaster 0.4.5

find antimcirobial resistance genes on genomes

ResBlaster

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Installation

pip3 install ResBlaster

Dependency

• BLAST+ >2.7.0

• cvmblaster (v0.4.1)

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>

Author: Qingpo Cui(SZQ Lab, China Agricultural University)

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
  -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>
  -updatedb UPDATEDB    <add input fasta to BLAST database>

ResBlaster subcommand:
  {show_db,init,updatedb}
    show_db             <show the list of all available database>
    init                <initialize the reference database>
    updatedb            <add custome database, use ResBlaster updatedb -h for help>

2. Show available database

ResBlaster show_db

DB_name	No. of seqs	Update_date
ESBL	1101	2024-10-09
LGI	1255	2024-07-31
bacmet1	578	2024-10-09
bacmet2_exp	753	2024-10-09
bacmet2_pred	155512	2024-10-09
lmo	20195	2024-10-09
ncbi	6146	2024-10-09
resfinder	3154	2024-10-09
rpoB	1	2024-10-09
ssuis_vf	111	2024-10-09
vf_hps	49	2024-10-09
vfdb_core	4329	2024-10-09
vfdb_full	32164	2024-10-09
vibrio_vf	5	2024-08-25

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:

>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 -updatedb owndb.fsa