Hi, I'm pretty new with metagenomics and my lab is using Illumina sequencing for generating an amplicon for purposes similar to 16S (OTU assignment) but using another marker which is longer (~580bp). The problem is that after getting the reads from MiSeq (2x300), the quality goes down after the 150 cycle and many of the reads had to be trimmed. The biggest problem is that most of the ends don't overlap, and one single end is not giving enough for blasting. Is there any tool that I can use to merge both ends? (I know there is going to be a gap, but I'd like at least to concatenate the sequences).
Thanks
Thanks
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