kevfengler227

yes, with HiCanu I do recover 2-3 contigs per plastid. Maybe the "uncorrected" plastid reads do assemble a bit but are filtered out because of high coverage. In general I...

I typically discard contigs smaller than 50 kb, so they may be lost that way. However, it is still suspicious that the plastid reads appear un-corrected and the coverage in...

OK, thanks. All of that makes sense. With those obstacles in mind, two strategies that would probably work to recover the plastids with hifiasm is to either 1) instead of...

I have had good success lately assembling the plastids with default parameters when I subset the target reads to 30-100x (after aligning to a reference). Without a reference, you can...

Sorry, I responded to the later comment. Just use the longest subset of reads to give ~50x. Also, like any other assembly you need to filter for contigs that have...

It would be a difficult problem to solve because the amount of chloroplast /mitochondrion can vary considerably with each DNA prep. We see ranges of 500-2000x and to an assembler...

So will setting --n-hap 3 produce a three haplotype assembly? I was just about to post a question about tetraploid assembly so I want to try --n-hap4 with hic. Thanks,...

OK, thanks. Polyploids are definitely the next challenge to overcome. I'll look forward to this capability in hifiasm as I have a lot of polyploids to do! KF