PyMLST - A Python Mlst Local Search Tool¶

PyMLST is used to perform core or whole genome Multilocus Sequence Typing. The bundle packages the dependencies required by PyMLST, see the table below for the versions of the included dependencies.

Software	Version
kma	1.3.23
mafft	7.505
pymlst	2.1.3
ucsc-blat	366

UFS HPC Usage Example¶

PyMLST can be used by first loading the module in the terminal.

1	`module load pymlst`

After loading the module, the following commands can be run in the terminal:

pyMLST
wgMLST
claMLST
kma
blat
mafft

The pymlst_shell commmand can be used to access a shell in the pymlst bundle.

1	`pymlst_shell`

Performance Notes¶

No performance notes available

Recommended resources per session¶

No recommended resources available

Benchmarks¶

No benchmarks available.

UFS HPC Community Guides and Tutorials¶

No community guides available.

Official site and documentation¶

Licensing Information¶

pyMLST is licensed under the GNU General Public v3 (GPLv3).

Primary citation¶

External Guides and Resources¶

If you know of a guide/tutorial that you have found useful, please help us share it by contacting the HPC staff at hpc@ufs.ac.za