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HongzheGuo / deBGA

de Bruijn Graph-based read aligner
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Effect of kmer size on mapping accuracy #1

Closed ulah closed 7 years ago

ulah commented 7 years ago

Hi, I'd like to evaluate deBGA for some single cell WGS data I have. Unfortunately, the biggest machine I have access to has 64GB RAM which is slightly below your posted mem footprint for hg19. I'd suppose that decreasing the kmer size will decrease the mem footprint. Can you tell how much mapping accuracy will be influenced by decreasing the kmer size from (let's say) the recommend 22 to 21 or 20? Btw: in the posted readme on github you write "-k parameter is restricted to 21-28 bp", but the program runs actually with any value. Cheers

ulah commented 7 years ago

I got access to another machine. Hence, this is not an issue for me anymore, thanks.