search

ruanjue / wtdbg2

Redbean: A fuzzy Bruijn graph approach to long noisy reads assembly
GNU General Public License v3.0
504 stars 92 forks source link

issue with visualising GFA using bandage #208

Closed unnatisonawala closed 3 years ago

unnatisonawala commented 4 years ago

Hello,

I want to view the assembly graph using bandage. I have converted the prefix.ctg.dot file to GFA using wtdbg-dot2gfa.pl, but when I try to use the resulting file in bandage I get the following error: 'GFA file contains links with complex CIGAR strings (containing operators other than M). Bandage does not support edge overlaps that are not perfect, so the behaviour of such edges in this graph is not defined.' What do you suggest?

ruanjue commented 4 years ago

Was it a problem of GFA different version? I haven't viewed the assembly graph.

jflot commented 3 years ago

It looks like the problem is that the GFA contains "0S" as a CIGAR string for contigs that do not overlap. Other assemblers that produce GFA (e.g., Flye) return "0M" in such case. If I replace "0S" with "0M" in the GFAs I obtain using wtdbg-dot2gfa.pl (using e.g sed -i 's/0S/0M/' *.gfa), I can open them in Bandage without problem ("S" in CIGAR normally stands for soft clip).

unnatisonawala commented 3 years ago

Thank you, will try that.