cvmcgmlst 0.1.6

cgMLST analysis tool

cvmmlst

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

usage: cvmcgmlst -i <genome assemble directory> -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. Could not use with -f
  -f F            <input_file>: the PATH of assembled genome file. Could not use with -i
  -db DB          <database_path>: path 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
  -create_db      <initialize the reference database>
  -t T            <number of threads>: default=8
  -v, --version   Display version

Installation

Using pip

pip3 install cvmcgmlst

Using conda

comming soon...

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

Making your own 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
TTAACAATTACGGCTCCAAATGAATTCGCCCGTGATTGGTTAGAATCTCATTATTCAGAG
CTAATTTCGGAAACACTTTATGATTTAACGGGGGCAAAATTAGCTATTCGCTTTATTATT
CCCCAAAGTCAAGCTGAAGAGGAGATTGATCTTCCTCCTGCTAAACCAAATGCAGCACAA
GATGATTCTAATCATTTACCACAGAGTATGCTAAACCCAAAATATACGTTTGATACATTT
GTTATTGGCTCTGGTAACCGTTTTGCTCACGCTGCTTCATTGGCCGTAGCCGAAGCGCCA
GCTAAAGCATATAATCCCCTCTTTATTTATGGGGGAGTTGGACTTGGAAAAACCCATTTA
ATGCATGCAATTGGCCATTATGTAATTGAACATAACCCAAATGCCAAAGTTGTATATTTA
TCATCAGAAAAATTTACAAATGAATTCATTAATTCTATTCGTGATAATAAAGCGGTCGAT
TTTCGTAATAAATACCGCAATGTAGATGTTTTATTGATAGATGATATTCAATTTTTAGCG
GGAAAAGAACAAACTCAAGAAGAGTTTTTCCATACATTCAATGCATTACACGAAGAAAGT
AAACAAATTGTAATTTCCAGTGATCGGCCACCAAAAGAAATTCCAACTTTAGAAGATCGT
CTTCGTTCTCGCTTTGAATGGGGACTCATTACGGATATTACGCCACCAGATTTAGAAACA
CGAATTGCGATTTTACGTAAAAAGGCAAAGGCTGAAGGACTTGATATACCAAATGAGGTC
ATGCTTTATATCGCAAATCAAATCGATTCAAATATTCGTGAACTAGAAGGTGCACTCATC
CGCGTTGTAGCTTATTCATCTTTAATTAACAAGGATATTAATGCTGATTTAGCAGCTGAA
GCACTTAAAGATATTATTCCAAATTCTAAACCAAAAATTATCTCCATTTATGATATTCAA
AAAGCTGTTGGAGATGTTTATCAAGTAAAATTAGAAGATTTCAAGGCGAAAAAGCGCACA
AAGTCAGTTGCCTTTCCTCGCCAAATTGCAATGTATTTGTCACGCGAACTGACAGATTCC
TCCTTACCTAAAATAGGTGAAGAATTTGGTGGACGTGATCATACAACCGTTATCCATGCC
CATGAAAAAATTTCTAAGCTACTTAAGACGGATACGCAATTACAAAAACAAGTTGAAGAA
ATTAACGATATTTTAAAGTAG

The first time when running cvmcgmlst, you should use -create_db parameter to initialize your database. After your own database was created, you could run cvmcgmlst without using -create_db parameter.

You could also create reference database using makeblastdb command.

makeblastdb -hash_index -in reference.fa -dbtype nucl -title cgMLST -parse_seqids

Example

# Single Genome Mode
cvmcgmlst -f /PATH_TO_ASSEBLED_GENOME/sample.fa -create_db -db /PATH_TO_DATABASE/reference.fa -o PATH_TO_OUTPUT

# Batch Mode
cvmcgmlst -i /PATH_TO_ASSEBLED_GENOME_DIR -create_db -db /PATH_TO_DATABASE/reference.fa -o PATH_TO_OUTPUT