cvmcgmlst 0.2.5

cgMLST analysis tool

cvmcgmlst

cvmcgmlst is a tool developed based on the cvmmlst for core genome MLST analysis .

Usage: cvmcgmlst -i <genome assemble directory> -o <output_directory> -db database_name

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

options:
  -h, --help            show this help message and exit
  -i I                  <input_file>: the PATH of assembled genome file
  -db DB                <database_path>: name of cgMLST database
  -o O                  <output_directory>: output PATH
  -minid MINID          <minimum threshold of identity>, default=95
  -mincov MINCOV        <minimum threshold of coverage>, default=90
  -t T                  <number of threads>: default=8
  -v, --version         Display version

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

Installation

Using pip

pip3 install cvmcgmlst

Dependency

• BLAST+ >2.7.0

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. Create reference cgmlst database

Users could create their own core genome database. All you need is a FASTA file of nucleotide sequences. The sequence IDs should have the format >locus_allelenumber, where LOCUS is the loci name, ALLELENUMBER is the number of this allele. The curated core genome fasta file should like this:

>GBAA_RS00015_1
TTGGAAAACATCTCTGATTTATGGAACAGCGCCTTAAAAGAACTCGAAAAAAAGGTCAGT
AAACCAAGTTATGAAACATGGTTAAAATCAACAACCGCACATAATTTAAAGAAAGATGTA
AAGTCAGTTGCCTTTCCTCGCCAAATTGCAATGTATTTGTCACGCGAACTGACAGATTCC
TCCTTACCTAAAATAGGTGAAGAATTTGGTGGACGTGATCATACAACCGTTATCCATGCC
CATGAAAAAATTTCTAAGCTACTTAAGACGGATACGCAATTACAAAAACAAGTTGAAGAA
ATTAACGATATTTTAAAGTAG
>GBAA_RS00015_2
TTGGAAAACATCTCTGATTTATGGAACAGCGCCTTAAAAGAACTCGAAAAAAAGGTCAGT
AAACCAAGTTATGAAACATGGTTAAAATCAACAACCGCACATAATTTAAAGAAAGATGTA
TTAACAATTACGGCTCCAAATGAATTCGCCCGTGATTGGTTAGAATCTCATTATTCAGAG
CTAATTTCGGAAACACTTTATGATTTAACGGGGGCAAAATTAGCTATTCGCTTTATTATT
GCTAAAGCATATAATCCCCTCTTTATTTATGGGGGAGTTGGACTTGGAAAAACCCATTTA
>GBAA_RS00015_3
ATGCTTTATATCGCAAATCAAATCGATTCAAATATTCGTGAACTAGAAGGTGCACTCATC
CGCGTTGTAGCTTATTCATCTTTAATTAACAAGGATATTAATGCTGATTTAGCAGCTGAA
AAAGCTGTTGGAGATGTTTATCAAGTAAAATTAGAAGATTTCAAGGCGAAAAAGCGCACA
AAGTCAGTTGCCTTTCCTCGCCAAATTGCAATGTATTTGTCACGCGAACTGACAGATTCC
CATGAAAAAATTTCTAAGCTACTTAAGACGGATACGCAATTACAAAAACAAGTTGAAGAA
ATTAACGATATTTTAAAGTAG
...

After finish installation, you should first initialize the reference database using following command

cvmcgmlst create_db -file YOUR_REF.fasta -name DBNAME

2. Show available database

You could list all available databases using the show_db subcommand.

cvmcgmlst show_db

The shell will print available databases

DB_name	No. of seqs	Update_date
demo	1	2025-02-25
DBNAME	Number of locus	Date

Run with your genome

# Single Genome Mode
cvmcgmlst -i /PATH_TO_ASSEBLED_GENOME/sample.fa -db DBNAME -o PATH_TO_OUTPUT