# cvmcgmlst
cvmcgmlst is a tool developed based on the [cvmmlst](https://github.com/hbucqp/cvmmlst) for core genome MLST analysis .
```shell
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
```shell
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](http://82.157.185.121:22300/shares/BevQrP0j8EXn76p7CwfheA)
### 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:
```shell
>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
```shell
cvmcgmlst create_db -file YOUR_REF.fasta -name DBNAME
```
### 2. Show available database
You could list all available databases using the show_db subcommand.
```shell
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
```shell
# Single Genome Mode
cvmcgmlst -i /PATH_TO_ASSEBLED_GENOME/sample.fa -db DBNAME -o PATH_TO_OUTPUT
```
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