Hi, all.

I am trying to assemble CCS reads from PacBio with Miniasm. We used a bait library to enrich sequences of interest and expect that assembled reads would be about a few Mb. Canu was able to give what I wanted. But the outputs from Miniasm are all smaller than 0.5Mb (when converted to fasta). Has anyone tried Miniasm to assemble reads of a small size? How would I need to improve this?

Here is what I did:

minimap -Sw5 -L100 -m0  CCS_reads.fasta CCS_reads.fasta > CCS_reads.paf

miniasm -f CCS_reads.fasta CCS_reads.paf > reads.gfa

awk '/^S/{print ">"$2"\n"$3}' reads.gfa > reads.utg.fa

Thank you in advance.