metashot/containment

metashot/containment is a workflow for the containment estimation of genomes, proteomes, plasmids and other sequences in sequencing read sets using mash screen.

• MetaShot Home

Main features

• Input: single-end, paired-end sequences in FASTA/FASTQ formats (gzip compressed files also supported);
• genomes or sequences on which test the containment in FASTA or mash sketch formats;
• returns the multeplicity matrix (genomes x read sets).

Quick start (examples)

Install Docker (or Singulariry) and Nextflow (see Dependencies);

Example 1 - genomes containment in single-end or interleaved read sets

nextflow run metashot/containment \
  --reads 'reads/*.fastq.gz' \
  --db 'genomes/*.fa' \
  --outdir results

Example 2 - genomes containment in paired-end read sets

nextflow run metashot/containment \
  --reads 'reads/*_R{1,2}*.fastq.gz' \
  --db 'genomes/*.fa' \
  --outdir results

Example 3 - sequences containment in paired-end read sets

nextflow run metashot/containment \
  --reads 'reads/*_R{1,2}*.fastq.gz' \
  --db sequences.fa \
  --individual \
  --outdir results

Parameters

Options and default values are decladed in nextflow.config.

System requirements

Please refer to System requirements for the complete list of system requirements options.