mash_screen

Purpose

This component performes mash screen to find plasmids contained in high throughoput sequencing data, using as inputs read files (FastQ files). Then, the resulting file can be imported into pATLAS. This component searches for containment of a given sequence in read sequencing data. However, this process can be user for other purposes, by providing a different database than the default that is intended for plasmid searches.

Note

  • pATLAs documentation can be found here.
  • MASH documentation can be found here.

Input/Output type

  • Input type: FastQ
  • Output type: JSON

Parameters

  • noWinner: A variable that enables the use of -w option for mash screen. Default: false.
  • pValue: P-value cutoff for the distance estimation between two sequences to be included in the output. Default: 0.05.
  • identity: The percentage of identity between the reads input and the reference sequence. Default: 0.9.
  • refFile: “Specifies the reference file to be provided to mash. It can either be a fasta or a .msh reference sketch generated by mash. Default: ‘/ngstools/data/patlas.msh’.

Published results

  • results/mashscreen/: A JSON file that can be imported to pATLAS with the results from mash screen.

Published reports

None.

Default directives

  • mashScreen:
    • container: tiagofilipe12/patlasflow_mash_screen
    • version: 1.1
  • mashOutputJson:
    • container: tiagofilipe12/patlasflow_mash_screen
    • version: 1.1