MLST

1 Overview | 2 Using | 2.1 Basic Command Line

Overview

Multilocus Sequence Typing (MLST): Multilocus sequence typing is a technique in molecular biology for the typing of multiple loci. The procedure characterizes isolates of microbial species using the DNA sequences of internal fragments of multiple housekeeping genes

Please read through the above site to understand how to download and set up the required database: MLST DB.
- This database has not been installed alongside MLST since it is not static and does update on a semi-regular basis.
  - It is expected that a user will download and set up the database locally using the species they need.
- If the usage of the software increases and the demand warrants the managing of a central database then please open up a consultation with ARCC.

Using

Use the module name mlst to discover versions available and to load the application.

Currently, MLST has only been tested on Singularity 2.5.2 (which is autoloaded). It will be tested using 3.1.1 in the future.

Basic Command Line

[]$ mlst
usage: mlst.py [-h] -i INFILE [INFILE ...] [-o OUTDIR] -s SPECIES
               [-p DATABASE] [-t TMP_DIR] [-mp METHOD_PATH] [-x] [-q]
mlst.py: error: the following arguments are required: -i/--infile, -s/--species

Test Example: Used an absolute path to link to the database using the -p option.

[]$ mlst -i 1056_genome_quiv2_HGAP3.fasta -s ecoli_2 -p /home/username/mlst_db/

Example Output

{
    "mlst": {
        "user_input": {
            "file_format": "fasta",
            "organism": "Escherichia coli#2",
            "species": "ecoli_2",
            "filename": [
                "1056_genome_quiv2_HGAP3.fasta"
            ]
        },
...
                }
            },
            "sequence_type": "2",
            "notes": ""
        }
    }
}