De novo small RNA assembly

[Juulluu21]

Hello,

I want to de novo assembly 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?

Thanks
-Juulluu21

[colindaven]

Sounds tricky - have you tried tadpole - listed on this forum - yet ?

[GenoMax]

Cross-posted and answered by @Brian: https://www.biostars.org/p/198427/