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ruanjue / wtdbg2

Redbean: A fuzzy Bruijn graph approach to long noisy reads assembly
GNU General Public License v3.0
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Extremely Low Coverage Assembly #170

Closed chocotwig closed 4 years ago

chocotwig commented 4 years ago

Hi,

Im trying to get at the rough structure of a genomic region. My coverage of this region is extremely low (3x). I simply want to see how my reads stack up with one another, I don't need high-confidence assembly. What would be a good way to stitch together these very low coverage reads? Even if there is a 2-read contig, that is sufficient. My reads are quite long (N50 35kb), using nanopore.

I have been using: -x ont -t 16 -S 1 -l 1000 --edge-min 1 --rescue-low-cov-edges -R --no-read-clip --aln-dovetail

Thanks!

ruanjue commented 4 years ago

there looks a missing

-x ont -t 16 -S 1 -l 1000 --edge-min 1 --rescue-low-cov-edges -R --no-read-clip --aln-dovetail -1
chocotwig commented 4 years ago

Okay! Do you recommend any changes to this?

Thanks!

ruanjue commented 4 years ago

It looks ok.