I would like to reconstruct my environemental 16S PCR fragments (slightly more than 300 bp) from my paired end reads (illumina, 250bp). I have good quality reads (more than 200 bp in length) from both ends of the original fragments and they should overlap well to reconstruct the ~300 bp originals.
Is there a tool in galaxy that would do this job...that is, overlap the two paired ends to make/reconstruct one fragment. If not, what is the best tool available elsewhere to do the job?
I will greatly appreciate any commnets and suggestions!