metamlst

Purpose

Checks the ST of metagenomic reads using mlst.

Note

Software page: https://bitbucket.org/CibioCM/metamlst

Input/Output type

  • Input type: FastQ
  • Output type: None

Note

The default input parameter for fastq data is --fastq.

Parameters

  • metamlstDB: Specifiy the metamlst database (full path) for MLST checking
  • metamlstDB_index: Specifiy the Bowtie2 metamlst database index (full path) for MLST checking

Published results

  • results/annotation/metamlst: Stores the results of the ST for each sample.

Published reports

None.

Default directives

  • container: flowcraft/metamlst
  • version: 1.1-1
  • memory: 4.Gb * task.attempt