generate fasta sequence from assembled reads

[Danielle Lema]

I need to generate fastas of the mitochondrial genome for use in software for generating haplotype networks (PopArt, Network), as these require sequence alignments as input.

I have used SOAP2 for reference guided assembly of my sequencing reads. I wonder, is there a way to compile the assembled reads from the output into a consensus sequence where each site represents the most frequently appearing base at that site across all reads scaffolded at that site? I basically want the sequence of the mitogenome as-is from the reads themselves (I do not expect there to be gaps as the breadth of coverage of the mitogenome for these samples was 100%, and as the mitogenome is only maternal, they are haploid, no need to worry about different alleles). I have been scouring for options, but I cannot seem to find any method that will just output the sequence of the reads as they have been assembled. Does anyone know if something like this exists?

Regards,

Danielle