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Old 06-11-2009, 05:50 PM   #23
Lesley
Junior Member
 
Location: New Zealand

Join Date: Jan 2008
Posts: 8
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Hi all,
I am just beginning to evaluate CLC Genomic Workbench for use with Illumina output and I am finding it so 454 orientated that it is driving me crazy with irrelevant instructions. Does anyone have any clear instruction on sorting Illumina based indexed sequencing?

The other question is - can we do real mapping with CLC or are we stuck with contig assembly (with or without reference). I do a lot of work with small ncRNAs and cannot find any tools in the trial that are remotely useful. I also find the comparison of their assembler with maq and soap a laugh, this is comparing an assembler with mappers.
I am working under an ubuntu 64 bit environment and the data loading of one lane of Paired End reads was extremely slow.

So far I feel the reality is not living up to the hype or maybe I am penalised for not working with human/mouse/rat resequencing data. Does anyone know if there are any tutorials on the NGS part of CLC bio that are relevent to indexed Illumina data or that from miRNAs?
By the way, thanks for the Velvet comparison. So far that has been the best de novo assembler for our group.

Cheers,
Lesley
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