Closed paoloshasta closed 1 year ago
Regarding mixing R10 reads with a small amount of coverage in R9 UL reads: Shasta is designed and written under the assumption that only one type of read is present, and does not do well in hybrid situations with mixed read types. For your situation, a possible way to proceed is to do a phased assembly using only the R10 reads. That would give pretty small phased bubbles, and you could then try and use some other tool (for example https://github.com/rlorigro/GFAse) to do additional phasing using the UL reads. But I know this suggestion is untested and a bit vague.
For the Shasta phased assembly you would use --config Nanopore-Phased-R10-Slow-Nov2022.conf
if your reads were generated at 260 bases per second ("slow") or --config Nanopore-Phased-R10-Fast-Nov2022.conf
if your reads were generated at 400 bases per second ("fast").
You could still try a Shasta assembly feeding it all the reads, and using those same assembly configurations. But I doubt that it would do much better than the assembly that uses only the R10 reads. Without UL reads, the portion of sequence assembled diploid wil probably be small, unless this cell line is highly heterozygous.
Regarding triploid sequence: Shasta phased assembly works under a diploid assumption, and so it will not be able to phase those regions. The assembly graph can still contain those regions, but they will not be phased and the assembly graph in those regions could be messy.
I am closing this due to lack of discussion. Feel free to reopen it or create a new issue if additional topics emerge.
@Aline-git posted the following in #1