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mlst

mlst scans contig files against traditional PubMLST typing schemes. The bundle packages version 2.23.0.

Usage example

The following command can be executed in the terminal to load the bundle:

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module load mlst

The module makes the following commands available:

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mlst
mlst-consistency_checker
mlst-download_pub_mlst
mlst-make_blast_db
mlst-show_seqs
mlst-ST_mini_genomes

The mlst_shell command can be used to access a shell in the bundle.

Run pet list -t mlst for a list of examples.

Performance notes

No performance notes available

mlst should be run on a system with at least 32 GB of RAM and 8 threads. Taken from paper Computational protocol for analyzing whole-genome sequencing data from Staphylococcus aureus clinical isolates.

Benchmarks

No benchmarks available.

Community guides and tutorials

  • No community guides available.

Official site and documentation

Licensing information

mlst is licensed under the GPLv2 license.

Primary citation

Seemann T, mlst Github

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