short read aligner with 3 mismatch and one gap allowed

[NicoBxl]

Hi,

Is there an short read (~25 nt) aligner that lets you specify the number of mismatch and number of gaps (and maybe the maximum length of the gap ? ) ?

Thanks,

N.

[Nicolas]

Bowtie2?
Novoalign?

[zee]

Novoalign does support gap open and gap extension penalties. Finding the right balance of these with your data is something you might think about doing. The defaults are set quite conservatively as with most other tools that perform a similar function.
Also do remember that allowing more gaps/mismatches can potentially drop your specificity.