quast

name	quast
description	Assembly quality assessment (contiguity, misassemblies; metaQUAST for metagenomes). Use this skill when working with quast: installing, choosing parameters, running commands, interpreting outputs, or troubleshooting. Upstream: https://github.com/ablab/quast. For stage routing use tool-selection / metagenomics-workflow.
license	MIT
category	analysis-tools
tags	["assembly","qc","quast"]
upstream	https://github.com/ablab/quast
stage	assessment

QUAST / metaQUAST

Upstream: QUAST / metaQUAST

Citation

Mikheenko, A., Saveliev, V. & Gurevich, A. MetaQUAST: evaluation of metagenome assemblies. Bioinformatics 32, 1088–1090 (2016). https://doi.org/10.1093/bioinformatics/btv697

See also docs/references.md.

Analytical thinking

Run after assembly before heavy binning to catch overly fragmented graphs. metaQUAST adds reference-based misassembly metrics when suitable genomes exist; without refs you still get contiguity stats (N50, length histograms).

Contiguity ≠ biological correctness. Do not choose assemblers on N50 alone — combine with mapping rate, bin recovery (mag-qc), and compute cost.

How to run

metaquast.py contigs.fa -o temp/quast -t 16
# or quast.py for generic stats without refs

Key parameters

Mode	When
metaquast.py	Metagenomes; optional reference set
quast.py	Quick contiguity without refs
Threads -t	Scale with CPU

Decision tree

Assembly assessment?
├─ Have references → metaQUAST
├─ No refs → QUAST stats + downstream bin QC
└─ CAMI gold standards → cami / AMBER (not QUAST alone)

Related skills

megahit · metaspades · metaflye · metamdbg · mag-qc · cami · tool-selection