kevfengler227

plastids don't assemble?

15

I have noticed that the chloroplast and mitochondrion do not assemble with hifiasm. I am not expecting to get the full plastid assembled correctly, but I don't see anything. When...

feature request to feed FALCON single FASTA

1

I’d like to put in a feature request to have FALCON accept a single FASTA in the input.fofn. This would be lot more convenient in many ways, particularly for large...

Accuracy in regions with only ONT support?

3

One of the key benefits of adding ONT to a PacBio HiFi assembly is to fill in the all the gaps arising from GA(n) coverage drop outs. Thus, in these...

feature request: filter reads with kmers from bam file?

6

Would it be possible to add a feature to run meryl-lookup exclude/include on a BAM instead of a fasta and output BAM? This would be very useful for filtering reads...

I am trying to figure out the best way to handle chimeric assembly errors that can occur in long SSRs in HiFi only assemblies for high-throughput applications. In the example...

v0.10.0b not available in conda

10

Can you add the lastest version of chopper to conda? I have been looking for a tool that is capable of trimming high quality segments from ONT reads. There is...