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Old 04-20-2011, 03:15 PM   #1
JackieBadger
Senior Member
 
Location: Halifax, Nova Scotia

Join Date: Mar 2009
Posts: 381
Default Numerous short read aligners: But which is best?

Hi All,

There seems to be a bunch of competing packages out there (MIRA3, Abyss, Velvet, Bowtie etc), but I wonder if anyone can offer a comparative synopsis of the data produced by each?

Has anyone compared assemblies between these packages, and which did they find most robust/reliable/erroneous/automated etc/?

My interests at the moment surround transcripome assemblies, and have been using MIRA3 and Geneious (which i think uses Bowtie). The incorporation of QUAL files in MIRA3 assemblies seems like a good idea.
Any thoughts?

Cheers,

J
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