I want to assemble a region of a bacterium genome (~10kb). The sequenced dna is from a single species, cultured from a single clone.
By now, I've mapped the reads (Illuminma PE150) to reference, assembled using spades (SE mode) with reads (not all paired) retrieved by samtools, and the assembly graph generated using Bandage using with
.gfa file is below:
I've manually checked the "bubles", and almost of them are very similar (99%) except of 1-2bp mismatches. And the depths of the two paths of the "bubles' are almost half to half, so they may not be sequence error.
By the way, the sequenced dna is from a single species, cultured from a single clone.
So, how can I get consensus sequence from this GFA graph? It's kind of like diploid genome, but I'm not familiar with this.
Thank you in advance.