For my first post on BioStars, I would like to ask a question.
I used an assembly pipeline based on SOAP-denovo to produce a few thousand contigs from Illumina PE-reads.
I noticed that some contigs overlap on the 5' or 3' ends by just a few BPs (4-25 nt) . When I compare to sequences from a close species I can see that it really makes sense to join them.
I tried SSPACE but it makes scaffolds full of Ns. I just need to do contig joining one terminal overlaps, any idea ?
Thank you for suggestions.