Which assembler for de-novo Illumina transcriptome assembly with relatively few reads

[kmkocot]

Hi all,

I am intersted in doing some relatively small transcriptome sequencing projects (1/12 of an Illumina HiSeq 2000 lane / transcriptome with unidirectional 100bp reads). The libraries that would be sequenced are double-stranded cDNA that were reverse transcribed with a polyA oligo. I was wondering if anyone has a feel for which of the leading short-read assembly programs (ABySS, CASAVA, VELVET/OASES, etc.) are best for de-novo assembly of such transcriptome projects?

Thanks!
Kevin

[lexa]

I would suggest you test the different programs. my experiences are that there is not THE BEST program to solve this problem. I got very good results using SOAPdenovo or Velvet/Oases for RNA-seq assemblies.