Generate consensus from contig alignment to reference sequence

Question

[daewowo]

I have been trying to find a method to extract a consensus from de-novo assembled contigs against a reference genome. This is how I currently do this:

De-novo assemble the dataset. Identify sequence of interest in it. Run bowtie2/bwa mem to align the contigs against a reference genome of interest. Use igv to extract consensus.

Is there any other tool that can generate a consensus sequence from contigs and a reference genome?

[desouzareis.r]

Hi,

Have you looked at this post? It may help.