This component performes mash screen to find plasmids contained in high throughout 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.
- Input type:
- Output type:
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 fastq or a .msh reference sketch generated by mash. Default: ‘/ngstools/data/patlas.msh’. If the component
mash_sketch_fastqis executed before this component, this parameter will be ignored and instead the secondary link between the two processes will be used to feed this component with the reference sketch.
results/mashscreen/: A JSON file that can be imported to pATLAS with the results from mash screen.