Colin Davenport

Thanks for looking at this! I would be happy with deleting the whole work directory, or just deleting the large(?) non-symlink files within the directory. In the meantime I have...

This kind of enhancement would also be great with dorado correct, since jobs are taking up to a week in my hands using 32 cores.

I think many people have this over-joined contigs problem at the moment with ont data. Certainly every `hifiasm --ont` assembly I have done so far has been overly -contiguous (evidence...

I think this is a problem for us despite the nice gains through dorado-correct. What I see is hugely improved contig N50s (from 37 -> 68 MB N50) for a...

The code works, we run it all the time. Can you not calculate the indices yourself if you have a server ? I'm not the dev.

Hi, yes, there was some discussion of adding papers here : https://github.com/colindaven/awesome-pangenomes/issues/8 I guess we should start adding the papers to the respective tools, since some tools are best described...

Hi @arpit20328 glad you're getting good results out of the tool. If you mask human reads then you will get less mappings to the human genome. This is assuming of...

Hi Arpit, I don't think you can turn off trimmomatic. We always ran it from raw sequence to avoid saving the trimmed. I can also advise you to use max...

That said, you can also comment out Lines 1541 -48 in the python script and see if that works for you (assuming paired end PE reads, there is a different...

The scrollbar idea is great. Even with Pacbio assemblies we are frequently going to be working with >100 reference sequences.