Whole genome assembly

[bair]

It might be a naive question:

After aligning agaist a reference genome, we can get sorted consensus sequences for each chromosome. My question is how to integrate the unmapped reads to generarte a distinct whole genome sequence?

Is De novo assembly of all the reads (mapped and unmapped, paired-end and single-end) doing this job?

Thanks

[Xi Wang]

It might be a naive question:

After aligning agaist a reference genome, we can get sorted consensus sequences for each chromosome. My question is how to integrate the unmapped reads to generarte a distinct whole genome sequence?

Is De novo assembly of all the reads (mapped and unmapped, paired-end and single-end) doing this job?

Thanks

I am afraid some of the unmapped reads are not from the genome, such as adaptors, or with too much sequencing errors.

[Ling]

Yes, I agree. And some of the unmapped reads may be DNA contamination from different species.

Ling

[Xi Wang]

Still, for whole genome assembly, you can try the tool - SOAPdenovo.

http://soap.genomics.org.cn/soapdenovo.html

[bair]

Thank you guys.

For whole genome, soapdenovo needs >150G RAM, that's expensive. worthy to try.