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ComparativeGenomicsToolkit / cactus

Official home of genome aligner based upon notion of Cactus graphs
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[WIP] s/SegAlign/KegAlign/g #1482

Closed glennhickey closed 2 months ago

glennhickey commented 2 months ago

This replaces SegAlign, which hasn't been maintained in years, with a newer fork called KegAlign. KegAlign promises better resource usage and, most importantly to cactus, ongoing maintenance which will hopefully help with interfacing and robustness issues.

As it stands, it's running on the small tests. I'll do some bigger runs on the cluster and post back results here before merging.

glennhickey commented 2 months ago

OK, I've run this on a 7 t2t apes and 12 zoonomia mammals, and results all seem to be as expected. I especially like the ability to control the number of CPUs, which we never had in segalign.