I want to de novo assembly of small RNA reads generated from Illumina sequencing (final lengths after clipping and trimming are 18-32nt).
Is there any pipeline available?
I tried Velvet. I used k-mer of 13 to 19 but could not assemble the reads. Assembled reads were maximum 70nt. My library is very deep and outstandingly overlapping (as most are piRNA). I really want to get the whole transcript (assembled).
Is any help out here?