SRST2: Short Read Sequence Typing for Bacterial Pathogens

Quick Links

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:

M.Inouye, H.Dashnow, L.-A.Raven, M.B.Schultz, B.J.Pope, T.Tomita, J.Zobel and K.E.Holt
SRST2: Rapid genomic surveillance for public health and hospital microbiology labs
Genome Medicine 2014, 6: 90

Documentation

SRST2 GitHub page

Important Notes

Module Name: SRST2 (see the modules page for more information)
Unusual environment variables set
- SRST2_HOME installation directory
- SRST2_BIN executable directory
- SRST2_SRC source code directory
SRST2 need to be run with python2.7, you can prepare a python 2.7 env with mamba and following command:
```
mamba create -n py27 python=2.7
mamba activate py27
        
```

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
|-- alleles_fasta
|-- profiles_csv
|-- mlst_data_download_Staphylococcus_epidermidis_None.log


0 directories, 4 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
|-- alleles_fasta
|-- profiles_csv
|-- mlst_data_download_Staphylococcus_epidermidis_None.log

0 directories, 4 files

End the interactive session:

[user@cn3200 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$