Need help for assemblying a high heterozygous genome! about wengan HOT 3 CLOSED

Hi bob,
Can you start the k-mer histogram from at least 10 of frequency? to see the peaks. A thing that you can do is to generate a short-read assembly with the Platanus assembler that is designed for highly heterozygous genomes (http://platanus.bio.titech.ac.jp/platanus/platanus-allee-2-0-was-released), then give that result as input to Wengan (-c option).

best,
Alex

from wengan.

Hi Alex,
Thanks very much for your timely advice. Given platanus is a memory greedy assembler, I am afraid it could not deal with such a big genome using our limited memory (~1Tb). The followed file is the distribution of 17mers altered as you suggested.
kmer_hist.pdf

Do you have any other advice?

Best,
Bob

from wengan.

Hi bob,

I think that if you feed only 50-60X coverage to Platanus the assembly might fit in 1TB machine.
There are other alternatives but are more complex to implement, so I suggest starting with Platanus first.

Best
Alex

from wengan.