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Old 11-09-2008, 06:26 PM   #5
lgoff
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Location: Cambridge, MA

Join Date: Feb 2008
Posts: 82
Default SOLiD

Originally, I was very put off by the SOLiD pipeline. It was initially very closed and there wasn't much I could do outside of the genome resequencing for which it was originally designed. The matching is relatively fast with SOLiD, but I do like the k-mer+Smith-waterman approach of SHRiMP. While the SOLiD pipeline has become much more robust. When we received our original machine, with the original cluster, it was underpowered for anything human. We had to re-develop our own pipeline for the specific applications we were using SOLiD for (smRNAs at the time). So we went with SHRiMP, and I have stuck with it since. Since we are lucky enough to be able to parallelize everything very nicely, the speed is not terribly an issue for us. I haven't tried the SOLiD pipeline in the past few months. Am I missing any dramatic improvements?
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