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fungi diploid genome denovo assembly by pacbio reads

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!

assembly
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updated by Ram Ram • written by orange • orange

2 answers

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

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written by orange • orange

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

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written by Rohit Rohit

Did you resolved your problem ?

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written by Picasa Picasa

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