ITADN

Feature Request: Support iterative MMseqs2 sensitivity search for the Annotate module

#180Opentimghaly 创建于 2026-04-22
T
timghalycommented
Dear geNomad team, thanks for this amazing tool! I would like to propose adding support for iterative MMSeqs2 sensitivity flags in the geNomad `annotate` module. Currently, users can set a sensitivity value (default -s 4.2), but for large metagenomic assemblies where higher sensitivity (e.g., -s 7.5) will help capture more divergent markers, the search becomes prohibitively slow. MMseqs2 supports an iterative approach (`--start-sens`, `--sens-steps`, and `-s`), where MMseqs2 starts searching with the lowest sensitivity defined with `--start-sens` and iteratively increases sensitivity only for query sequences with no hits in earlier iterations until the target sensitivity `-s` is reached. This can significantly speed up best-hit searches. I think that this could be a helpful addition to improve the sensitivity of geNomad without prohibitively slow runtimes. Thanks again for all the work you put into maintaining this awesome resource. Cheers, Tim
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