I am looking for a painless method for conducting a very small assembly of short sequences based on exact identity. Simply put, I have an NGS sample that I believe is contaminated with a common sequence. I scanned a few million reads and determined the top 50 most abundant kmers of length 25nt. Browsing these top 50 kmers, it is clear that they are mostly staggered windows of a single sequence, and I would like to assemble these 50 kmers by overlapping identity.
Short of writing a perl script, does someone know of a simple way to do this? Thanks!