Hi all,
I'm using SAOP de-novo to assemble reads of a bacteria. We assess that the size of the genome should be around 100 - 200 kbp.
We sequenced paired end reads 64bp X 2, and have a total of ~24M reads after filtering.
For some reason SOAP de-novo doesn't give good results. I tried to use different K-mer values. I either get a cover of 1.8 Mbp with about 5,900 scaffolds and singletons (Kmer = 61), or a cover of 20,000 bp with 46 scaffolds and singletons.
I also tried to put different map_len values (from 35 to 50) and it didn't change a lot.
Shouldn't this be a simple task for SOAP de-novo? If the assessment of the genome size is correct, I have a coverage of 120X ...
Why am I have problems?
Thanks in advance,
Rachelly.
I'm using SAOP de-novo to assemble reads of a bacteria. We assess that the size of the genome should be around 100 - 200 kbp.
We sequenced paired end reads 64bp X 2, and have a total of ~24M reads after filtering.
For some reason SOAP de-novo doesn't give good results. I tried to use different K-mer values. I either get a cover of 1.8 Mbp with about 5,900 scaffolds and singletons (Kmer = 61), or a cover of 20,000 bp with 46 scaffolds and singletons.
I also tried to put different map_len values (from 35 to 50) and it didn't change a lot.
Shouldn't this be a simple task for SOAP de-novo? If the assessment of the genome size is correct, I have a coverage of 120X ...
Why am I have problems?
Thanks in advance,
Rachelly.
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