fungi diploid genome denovo assembly by pacbio reads

Question

[orange]

Hi, everyone. I have a project about 50M fungi diploid denovo assembly. I had assembly 37M fungi haploid with pacbio reads and illuminate and Miseq reads. For haploid genome, I used Ectool and HGAP3. But for diploid genome, I have doubt about how to correct subreads, and which assembler to use.

And I have about 50x subreads.

Thanks!

Answer 1

[orange]

My firt thought is use SOAP2 to get diploid contigs,then use these contigs and PE reads to correct subreads ,inally use FALCON.

[Rohit]

PacBio self-error correction (PBcR) is possible at such high coverages. Then you can use Falcon assembler or CANU.

Answer 2

[Picasa]

Did you resolved your problem ?