XSQ format compatible denovo Transcript Assemblers

[Zainab]

Hello all,
We are working with SOLiD 5500 System. We want to assemble our denovo transcripts for a plant. We have come across a few assemblers compatible with XSQ format but we still need a good advice on XSQ compatible denovo transcripts assemblers. Thankyou.

[colindaven]

I don't know of anything here. de novo assembly is very tricky with SOLiD and actually doesn't work at all. You can expect very short transcript fragments (<1kbp, most ~200bp). Illumina works a lot better here.

I haven't tried it, but it might make more sense to map to a reference genome and then attempt to use cufflinks on the BAMs. Not de novo I know, but it might be more rewarding.