Post processing steps after SALSA

[pubudumanoj]

I ran SALSA and got the final fasta file. However, there are about 3000 scaffolds.

1. Is there a way to improve this to a chromosome level scaffold. How we can measure the quality of the scaffolding?
2. How we can generate some statistics other than stats from quast.
3. I created a hic file and visualized it using Juice box. But is there a way to correct misassemblies?

[ghuryejay]

1. Improving scaffolding is an open research question.
2. What kind of statistics you are looking to generate?
3. Currently we don't support misassembly correction for SALSA2 output through juicebox.