Sergey Koren

You can probably use the output of the juicer pipeline as well as the arima pipeline without marking duplicates since it's built into both pipelines. Feel free to post whether...

Unfortunately SALSA is only designed for python2 and there is no python3 version. It wouldn't be trivial to update since the networkx version it depends on is also meant to...

There isn't a way to group contigs beyond the scaffolding done in SALSA. If it didn't group them, then it likely reached the stopping condition where no useful links were...

It sounds like the scaffolds folder is missing some expected files required for conversion. What is the full contents of the scaffolds folder you're running on? There should be a...

I would expect sequential runs would work better. The issue with combining these libraries is they will have very different length distributions and I worry the selection of best edges...

@ghuryejay can confirm but I'm pretty sure the iteration parameter is no longer used. As described in the manuscript for SALSA2, the stopping condition is dynamically determined based on when...

We've never tested with the gfa from hifiasm so it may be some incompatibility. In general, the contig gfa isn't that useful for scaffolding information since most connectivity is removed...

I assume you're trying to run convert.sh and don't want to scaffold at all? You should be able to specify no mappings (an empty bed file) for scaffolding but this...

Unfortunately, we don't have the data organized by chromosome so your only option would be to download and extract the full set. If you have IDs of the reads you're...

You're running correction which should not use overlapInCore by default and so likely it hasn't been configured correctly/tested. It is definitely not recommended or supported to run overlapInCore for this...