Question: fungi diploid genome denovo assembly by pacbio reads
0
gravatar for orange
5.6 years ago by
orange30
Korea, Republic Of
orange30 wrote:

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 use which assembler .

And I have about 50x subreads.

 

Thanks!

assembly • 2.1k views
ADD COMMENTlink modified 4.7 years ago by Picasa570 • written 5.6 years ago by orange30
0
gravatar for orange
5.6 years ago by
orange30
Korea, Republic Of
orange30 wrote:

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

ADD COMMENTlink written 5.6 years ago by orange30
1

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

ADD REPLYlink written 4.6 years ago by Rohit1.4k
0
gravatar for Picasa
4.7 years ago by
Picasa570
Picasa570 wrote:

Did you resolved your problem ?

ADD COMMENTlink written 4.7 years ago by Picasa570
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