Problem: I have a multiple alignment of sequence reads. Each individual is represented by two sequences, forward and reverse (e.g.
individual1_Rev) that don't overlap at the ends. I want my alignment to have one sequence per individual that is the consensus of the forward and reverse sequences. NB I don't want to create a consensus across all individuals. I want to recognise sequences that share a name e.g. "individual1" and replace them with a full-length consensus of those two sequences.
Does anybody know of existing script or programs to do this? If it doesn't already exist I shall probably start putting something together with BioPerl, any suggestions of best approach?