CLC Genomics Workbench for de novo RNA-seq

[JQH]

Anyone have an expert opinion to share on the pros and cons of using CLC Genomics Workbench for de novo transcriptome assembly from 454 and Illumina paired end reads and mapping of Illumina reads to the assembly for digital expression values? I know that CLC uses RPKM (reads per kilobase of transcript per million mapped reads), which is not advantageous over FPKM, due to the potential for skewed data resulting from poor quality in read pairs. Any advice/opinions would be great.

[sisch]

Anyone have an expert opinion to share on the pros and cons of using CLC Genomics Workbench for de novo transcriptome assembly from 454

We do use CLC a lot for de novo assembly of 454 data. We even tested it against other assemblers and the results are published here. Short version is, that CLC and TGICL show the best assembly quality, but where TGICL takes days to weeks for assembly CLC is finished within minutes. Big "pro" for CLC here.

A "con" surely is, that CLC remains a black box, you can't really tell what it does in detail.

and mapping of Illumina reads to the assembly for digital expression values?

I personally prefer to have the mapping under my control, that's why I never use CLC for it. Instead I usually go for a very traditional approach with BLAST/BLAT and homemade perl scripts.

Cheers,
Simon