How To Generate Two Haplotypes Using Velvet

Question

[lyz10302012]

Hi everyone,

I use velvet to do de novo assembly on a particular region (in a bam file) and this region contain a heterozygous Indel. I think it should generate two contigs (represent two haplotypes of the genome), but it only generation one, can anyone explain it for me.

Answer 1

[zam.iqbal.genome]

It won't work, and it's not velvet's fault I'm afraid. That's not what velvet is trying to do. Its goal is to produce a whole genome consensus, not to distinguish haplotypes.