QUAST
Quality assessment tool for genome assemblies
The module parses the report.tsv files generated by
QUAST and adds key metrics to the report General Statistics table.
All statistics for all samples are saved to multiqc_data/multiqc_quast.txt.
Configuration
By default, the QUAST module is configured to work with large de-novo genomes, showing thousands of contigs, mega-base pairs and other sensible defaults.
If these aren't appropriate for your genomes, you can configure them as follows:
quast_config:
contig_length_multiplier: 0.001
contig_length_suffix: "Kbp"
total_length_multiplier: 0.000001
total_length_suffix: "Mbp"
total_number_contigs_multiplier: 0.001
total_number_contigs_suffix: "K"
The default module values are shown above. See the main MultiQC documentation for more information about how to configure MultiQC.
MetaQUAST
The QUAST module will also parse output from
MetaQUAST runs (metaquast.py).
The combined_reference/report.tsv file is parsed, and folders
runs_per_reference and not_aligned are ignored.
If you want to run MultiQC against auxiliary MetaQUAST runs, you must explicitly pass these files to MultiQC:
multiqc runs_per_reference/reference_1/report.tsv
Note that you can pass as many file paths to MultiQC as you like
and use glob expansion (eg. runs_per_reference/*/report.tsv).
File search patterns
quast:
contents: "Assembly\t"
fn: report.tsv
num_lines: 2