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Old 07-08-2008, 02:56 AM   #5
NGS specialist
Location: Malaysia

Join Date: Apr 2008
Posts: 249

I've been using novoalign as well and my bet is that ELAND should be faster than novoalign at default because novoalign will spend a little more time looking for those extra mismatches and gaps. At a threshold of 60 novoalign should be as fast as ELAND or perhaps a bit faster. ELAND achieves better performance because it indexes reads and does a fast scan of the genome.
Perhaps somebody would be willing to try it out. Take a few million paired-end/single-end reads and see how novoalign at threshold 60 would do in comparison to ELAND on the same server specification.
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