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EI-CoreBioinformatics / DToL_asm_hifi

Assembly (Hifi), Breaking (10X), Scaffolding (10X) and Polishing (10X) pipeline
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Functinality to run all currently installed hifi assemblers (instead of just hifiasm) #10

Open garethlin opened 3 years ago

garethlin commented 3 years ago

Sanger run both hifiasm and hicanu Perhaps a --both flag to do the same as Sanger and run these 2 assemblers (we got bad results with hicanu on marigold)

Perhaps an --all flag to run all we have installed (hicani, hifiasm, wtgbg2, IPA, Peregrine)

garethlin commented 3 years ago

It would also be possible to add --select-size and --select-n50 flags to choose for each sample out of al these assemblies based on best N50 or size closest to predicted genome size (predicted genome size is in the sample sheet)