Merge simple edges in the assembly graph?

voutcn / megahit

Ultra-fast and memory-efficient (meta-)genome assembler

http://www.ncbi.nlm.nih.gov/pubmed/25609793

GNU General Public License v3.0

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Merge simple edges in the assembly graph? #364

Open schorlton opened 9 months ago

schorlton commented 9 months ago

Hi @voutcn and @aquaskyline,

I ran megahit 1.2.9 and got the following graph with megahit_toolkit contig2fastg 141 final.contigs.fa:

Note the contig subgraphs I have highlighted in the red boxes - can I safely merge these? I am uncertain why they would have been generated as separate contigs. Thanks!!

schorlton commented 9 months ago

Also just stumbled across https://github.com/voutcn/megahit/issues/184 which looks similar