View Single Post
Old 01-17-2017, 02:34 PM   #50
Brian Bushnell
Super Moderator
Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,707

I don't really know where the high mutation rate comes from in supposedly isolate libraries. Unfortunately, there's no mechanism in Tadpole to fix them - it always halts at a branch and breaks into two contigs, even if it is a single SNP. You can use the "branchmult1" and "branchmult2" flags to adjust this, though. Dropping them to "bm1=6 bm2=2" can often substantially increase continuity. "bm1=6" means it will continue rather than stopping at a branch where the allele ratio of the next base is at least 6:1 rather than at least 20:1 which is the default. With an allele ratio of 1:1 like you have it will never continue, though. Instead, you might try a scaffolding program and gap-filling program that will use paired-end reads to glue the two contigs back together. I have not written one or tested any, but I know several are available.

"rinse" and "shave" can, in some cases, improve continuity by remove very low-depth errors, but that's not the case here. "shave=f" will not do anything, though. "t" and "f" stand for "true" and "false". The default for "shave" is already "false". So, you can try enabling these with "rinse shave" or "rinse=t shave=t" or "rinse=true shave=true", which are all equivalent.

Anyway - believe me, I would also prefer in your case for Tadpole to assemble this as a single contig, but it generally won't do that in the case of such evenly-split alleles. Though maybe with "bm1=1.1 bm2=1.05" it would; I'm not really sure what would happen in that case.
Brian Bushnell is offline   Reply With Quote