Biowulf High Performance Computing at the NIH
SRST2: Short Read Sequence Typing for Bacterial Pathogens

SRST2 is a a read mapping-based tool for rapid molecular typing of bacterial pathogens. It allows fast and accurate detection of genes, alleles and multi-locus sequence types (MLST) from WGS data. SRST2 is highly accurate and outperforms assembly-based methods in terms of both gene detection and allele assignment.

References:

Documentation
Important Notes

Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive 
[user@cn3200 ~]$ module load srst2   
[+] Loading bowtie  2-2.2.6
[+] Loading srst2 0.2.0  ...
Run a sample command:
[user@cn3200 ~]$ getmlst.py --species "Staphylococcus aureus"

  For SRST2, remember to check what separator is being used in this allele database

  Looks like --mlst_delimiter '_'

  >arcC_1  --> -->   ('arcC', '_', '1')

  Suggested srst2 command for use with this MLST database:

    srst2 --output test --input_pe *.fastq.gz --mlst_db Staphylococcus_aureus.fasta --mlst_definitions saureus.txt --mlst_delimiter '_'
The following files will be produced in the current folder:
[user@cn3200 ~]$ tree .
.
|-- Staphylococcus_aureus.fasta
|-- arcC.tfa
|-- aroE.tfa
|-- glpF.tfa
|-- gmk.tfa
|-- mlst_data_download_Staphylococcus_aureus_2019-08-20.log
|-- pta.tfa
|-- saureus.txt
|-- tpi.tfa
`-- yqiL.tfa

0 directories, 10 files
Run another sample command:
[user@cn3200 ~]$ getmlst.py --species "Staphylococcus epidermidis" --repository_url  http://pubmlst.org/data/dbases.xml

  For SRST2, remember to check what separator is being used in this allele database

  Looks like --mlst_delimiter '_'

  >arcC_1  --> -->   ('arcC', '_', '1')

  Suggested srst2 command for use with this MLST database:

    srst2 --output test --input_pe *.fastq.gz --mlst_db Staphylococcus_epidermidis.fasta --mlst_definitions sepidermidis.txt --mlst_delimiter '_'
The output files are as follows:
[user@cn3200 ~]$ tree .
.
|-- Staphylococcus_epidermidis.fasta
|-- arcC.tfa
|-- aroE.tfa
|-- gtr.tfa
|-- mlst_data_download_Staphylococcus_epidermidis_2019-08-20.log
|-- mutS.tfa
|-- pyrR.tfa
|-- sepidermidis.txt
|-- tpiA.tfa
`-- yqiL.tfa

0 directories, 10 files
End the interactive session:
[user@cn3200 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$