sequence alignment tool selection question

[slny]

Hi,

Currently I'm using bowtie for sequence alignment. It's fast, but what's the trade-off for the speed? Any suggestion for sequence alignment tool suggestion?

Thanks,
Slny

[pbluescript]

Without knowing anything about your sequencing platform, source material, etc. There's not much we can do to help.
Try these papers:

http://www.nature.com/jhg/journal/vaop/ncurrent/full/jhg201143a.html

http://www.biomedcentral.com/1471-2105/12/210

[HESmith]

You use BFAST, which implements a local alignment algorithm, or BFAST+BWA, which combines it with Burrows-Wheeler alignment. It allows the user to specify the parameters that trade-off speed for accuracy.