| 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
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
