| name | deepurify |
| description | Deepurify — multi-modal deep language model for MAG decontamination by matching contigs to taxonomic lineages and splitting chimeric bins into higher-quality sub-MAGs. Use when: (1) Cleaning contaminated MAGs after binning, (2) Rescuing near-threshold contaminated bins, (3) Complementing CheckM2/GUNC (detection vs contig removal). Upstream: https://github.com/ericcombiolab/Deepurify.
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| license | MIT |
| category | analysis-tools |
| tags | ["decontamination","MAG","Deepurify","QC"] |
| upstream | https://github.com/ericcombiolab/Deepurify |
| stage | assessment |
Deepurify
Upstream: ericcombiolab/Deepurify
Citation
Zou, B. et al. A multi-modal deep language model for contaminant removal from
metagenome-assembled genomes. Nat. Mach. Intell. 6, 1245–1255 (2024).
https://doi.org/10.1038/s42256-024-00908-5
See also docs/references.md.
Analytical thinking
CheckM2/GUNC score contamination; Deepurify aims to remove contaminant
contigs and split chimeras into sub-MAGs using sequence↔taxonomy multimodal
embeddings. Paper reports substantial gains in high-quality MAG counts across
soil, ocean, plant, freshwater, and human faecal sets — treat as
benchmark-conditioned.
Recommended order:
bins → checkm2 (± gunc)
→ deepurify on contaminated / borderline bins
→ re-QC with checkm2 / gunc
→ drep / gtdbtk
Do not skip re-QC after decontamination. Model errors can drop true contigs —
inspect high-value novel lineages manually (anvio).
How to run
deepurify \
-i bins/ \
-o temp/deepurify \
Decision tree
MAG contamination problem?
├─ Detect / filter only → checkm2 / gunc / mag-qc
├─ Remove contigs / split chimeras → deepurify
├─ Interactive contig surgery → anvio
└─ Prevent upstream → multi-coverage binning + ensemble (basalt ★)
Related skills
checkm2 · gunc · mag-qc · anvio · basalt · drep · tool-selection
