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ksahlin / strobealign

Aligns short reads using dynamic seed size with strobemers
MIT License
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strobealign-aemb module for metagenomic binning #394

Closed psj1997 closed 3 months ago

psj1997 commented 4 months ago

Hi,

This is the aemb (abundance estimation for metagenomic binning) module, the usage is :

strobealign ref.fa read1.fq read2.fq --aemb > abun.txt

In my benchmarking, aemb can output similar results, but decrease more than 90% running time.

Sincerely Shaojun

ksahlin commented 4 months ago

Thanks Shaojun. I think Marcel is a bit busy right now but I am sure he will have a look when there is sufficient time.

marcelm commented 3 months ago

This looks good now! I think this deserves a slightly longer section in the documentation, but I’ll do that after merging.