quast
Tags: assembly quality assessment metrics n50 evaluation sample-scope
Evaluate assembly quality using QUAST.
This subworkflow assesses genome assembly quality using QUAST (Quality Assessment Tool for Genome Assemblies). It provides comprehensive metrics including N50, L50, GC content, total length, and other quality statistics. The workflow generates both individual sample reports and a combined summary for comparative analysis across all assemblies.
Take
fasta: Channel<Record>
| Field | Description |
|---|---|
meta | Groovy Record containing sample information |
assembly | Assembled contigs in FASTA format (Path) |
meta_file | Meta file containing reference size information (Path) |
Emit
Published
The sample_outputs and run_outputs emissions are aggregates of output files that will be published in the entry workflow.
sample_outputs
| Output | Description |
|---|---|
tsv | Transposed report in TSV format |
supplemental | Supplemental files including plots and HTML reports |
run_outputs
| Output | Description |
|---|---|
csv | Aggregated results in CSV format |
Module Composition
This subworkflow calls the following modules:
- csvtk_concat - Concatenate multiple CSV or TSV files into a single table.
- quast - Quality Assessment Tool for Genome Assemblies.
Used By
This subworkflow is used by the following workflows:
- quast - Quality assessment of assembled contigs using QUAST.
Citations
If you use this in your analysis, please cite the following.
-
Bactopia
Petit III RA, Read TD Bactopia - a flexible pipeline for complete analysis of bacterial genomes. mSystems 5 (2020) -
QUAST
Gurevich A, Saveliev V, Vyahhi N, Tesler G QUAST: quality assessment tool for genome assemblies. Bioinformatics 29, 1072-1075 (2013)