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cvmmlst is a bacteria mlst analysis tool that could run on Windows, Linux and MAC os. Some of the code ideas in cvmmlst draw on Torsten Seemanns excellent mlst tool.
pip3 install cvmmlst
comming soon...
- BLAST+ >2.7.0
you should add BLAST in your PATH
Following this tutorial: Add blast into your windows PATH
The easyest way to install blast is:
conda install -c bioconda blast
After finish installation, you should first initialize the reference database using following command
cvmmlst -init
usage: cvmmlst -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
-o O <output_directory>: output PATH
-minid MINID <minimum threshold of identity>, default=90
-mincov MINCOV <minimum threshold of coverage>, default=60
-init <initialize the reference database>
-t T <number of threads>: default=8
-v, --version Display version
you will get a text file and a summray file in csv format in the output directory.
The text file like
| dat | bglA | cat | ldh | abcZ | dapE | lhkA | ST | Scheme | FILE |
|---|---|---|---|---|---|---|---|---|---|
| 3 | 1 | 4 | 39 | 12 | 14 | 4 | 87 | listeria_2 | 665 |
The content in csv summary file like
| dat | bglA | cat | ldh | abcZ | dapE | lhkA | ST | Scheme | FILE |
|---|---|---|---|---|---|---|---|---|---|
| 3 | 1 | 4 | 39 | 12 | 14 | 4 | 87 | listeria_2 | sample01 |
| 2 | 4 | 4 | 1 | 4 | 3 | 5 | 3 | listeria_2 | sample02 |
| 6 | 6 | 8 | 37 | 7 | 8 | 1 | 121 | listeria_2 | sample03 |
| 3 | 1 | 4 | 39 | 12 | 14 | 4 | 87 | listeria_2 | sample04 |
| 2 | 4 | 4 | 1 | 4 | 3 | 5 | 3 | listeria_2 | sample05 |
| 6 | 6 | 8 | 37 | 7 | 8 | 1 | 121 | listeria_2 | sample06 |
