dadaist2-mqc-report

dadaist2-mqc-report generates a MultiQC-ready folder starting from the data available in a Dadaist2 run where taxonomy was assigned.

An example report is available.

Synopsis

usage: dadaist2-mqc-report [-h] -i INPUT_DIR [-t TOPTAXA] -o OUTPUT_DIR

Produce multiqc report

optional arguments:
  -h, --help            show this help message and exit
  -i INPUT_DIR, --input-dir INPUT_DIR
  -t TOPTAXA, --toptaxa TOPTAXA
  -o OUTPUT_DIR, --output-dir OUTPUT_DIR

Description

Beside checking the execution logs, it's useful to have an overview of the whole experiment before performing accurate analyses.

Content of the report

  • DADA2 denoising statistics: how many input reads, filtered reads, denoised reads, merged reads and final reads after chimera removal
  • Octave plots to evaluate the distribution of the abundance counts
  • The most abundant FASTA sequences, both classified and unclassified
  • Taxonomic barplots at different levels

Usage

MultiQC is required, an it's automatically installed with the dadaist2-full package but not with the thinner dadaist2. See installation.

  1. Generate the report files: dadaist2-mqc-report -i DadaistOutput -o DadaistOutput/qc/
  2. Generate the report: multiqc -c DadaistOutput/qc/config.yaml DadaistOutput/qc/
  3. Open the report with a browser (will be multiqc_report.html in the output folder)