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marbl / SALSA

SALSA: A tool to scaffold long read assemblies with Hi-C data
MIT License
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-u no longer available #106

Closed malonge closed 4 years ago

malonge commented 4 years ago

Hi there,

It looks like the -u option has been removed since v2.1. Since I assume it is no longer supported, what is your advice for scaffolding Canu unitigs?

I was originally thinking I would set the following parameters

-a asm.unitigs.fasta
-g asm.unitigs.gfa
-u asm.unitigs.bed

I suppose I could just use the contigs instead, but then I think Salsa can't utilize an assembly graph, since HiCanu doesn't provide a graph for contigs. Is that right?

Thanks in advance, Mike

malonge commented 4 years ago

Or maybe I should just exclude -u and use stitch.py to bring in the contig information after the fact?

ghuryejay commented 4 years ago

You are right. You should use stitch.py to bring unitig to contig information after scaffolding.

malonge commented 4 years ago

Thanks!