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Old 04-20-2011, 03:15 PM   #1
JackieBadger
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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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Old 04-20-2011, 06:17 PM   #2
nilshomer
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See: http://assemblathon.org/
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Old 04-20-2011, 09:19 PM   #3
kokonech
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Evaluation of asssembly algorithms
http://gage.cbcb.umd.edu/

BTW, MIRA3 is de novo assembly, while Bowtie is short read aligner. Not sure, but I think Geneious use their own algorithm.
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Old 04-21-2011, 02:17 AM   #4
JackieBadger
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cheers, guys

j
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Old 04-28-2011, 11:02 AM   #5
Geneious
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Hi, Yes, Geneious uses its own algorithm inside Geneious Pro, however Geneious Server allows users on the desktops to run a range of different mappers and assemblers including SOAP2, BWA, MAQ, Bowtie and Velvet in addition to the Geneious Reference Assembler and the Geneious de novo Assembler
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