skoren
commented
7 years ago Generally, there's a couple of ways of dealing with the ploidy. Our preferred method is to avoid collapsing the genome so you end up with double (or triple) the genome size as long as your divergence is above about 2% on average. Below this divergence, you'd end up collapsing the variations. The main thing is that your genome is about three times larger than the haploid size so you want higher coverage for assembly. We've used the following parameters for recent polyploid insect populations with good results (assuming you're using PacBio data0:
corOutCoverage=200 errorRate=0.013 "batOptions=-dg 3 -db 3 -dr 1 -ca 500 -cp 50"
This will output more corrected reads (than the default 40x since that would only be <15x per haplotype). The latter option will be more conservative at picking the error rate to use for the assembly to try to maintain haplotype separation. If it works, you'll end up with approximately 3x your haploid genome size. You'll have to do post-processing using gene information or other synteny information to remove the redundancy in this assembly since you'll have 3 copies of large parts of the genome.
The alternative is to try to smash everything together and then do phasing using another approach (like HapCUT2 or whatshap or others). In that case you want to do the opposite, increase the error rate:
corOutCoverage=200 ovlErrorRate=0.15 obtErrorRate=0.15
I will add these options to the documentation.
brianwalenz
lamz138138
Hi, Does Canu have any settings for polyploidy? We trying to assemble a triploid.
Thank you in advance.
Michal