MLST

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MLST Multi-Locus Sequence Typing
Please read through the above site to understand how to download and setup 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. So, currently it is expected that a user will download and setup 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.

Module: Example

[]$ module spider mlst
--------------------------
  mlst: mlst/2.0.4
--------------------------
    You will need to load all module(s) on any one of the lines below before the "mlst/2.0.4" module is available to load.

      singularity/2.5.2
      singularity/3.1.1
 
    Help:
      The MLST service contains one python script mlst.py which is the script of the lates version of the MLST service. 
      The method enables investigators to determine the ST based on WGS data.
      https://bitbucket.org/genomicepidemiology/mlst/src/master/

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

[]$ module load mlst/2.0.4

Using:

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": ""
        }
    }
}

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