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-   -   short read aligner with 3 mismatch and one gap allowed (http://seqanswers.com/forums/showthread.php?t=15380)

NicoBxl 11-09-2011 03:34 AM

short read aligner with 3 mismatch and one gap allowed
 
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 11-09-2011 07:07 AM

Bowtie2?
Novoalign?

zee 11-09-2011 10:26 AM

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.


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