| name | drep |
| description | Dereplicate microbial genomes by ANI to species/strain catalogues. Use this skill when working with drep: installing, choosing parameters, running commands, interpreting outputs, or troubleshooting. Upstream: https://github.com/MrOlm/drep. For routing across tools, use tool-selection. For end-to-end pipelines, use metagenomics-workflow.
|
| license | MIT |
| category | analysis-tools |
| tags | ["dereplication","ANI","MAG"] |
| upstream | https://github.com/MrOlm/drep |
dRep
Upstream: MrOlm/drep
Citation
Olm, M. R., Brown, C. T., Brooks, B. & Banfield, J. F. dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. ISME J. 11, 2864–2868 (2017). https://doi.org/10.1038/ismej.2017.126
See also docs/references.md.
Analytical thinking
dRep collapses redundant MAGs into representatives. -sa 0.95 ≈ species;
-sa 0.99 ≈ strain-level. Quality filters (-comp/-con) silently drop
genomes—align them with checkm2 / mag-qc policy.
For >~20k genomes, --ignoreGenomeQuality may be needed; then run CheckM2
separately.
How to run
dRep dereplicate temp/drep95/ -g bins/*.fa \
-sa 0.95 -nc 0.30 -comp 50 -con 10 -p 16
Related skills
metawrap · basalt · checkm2 · coverm · gtdbtk
