Numerous short read aligners: But which is best?

[JackieBadger]

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

[nilshomer]

See: http://assemblathon.org/

[kokonech]

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.

[JackieBadger]

cheers, guys

j

[Geneious]

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