short read aligner with 3 mismatch and one gap allowed

NicoBxl · 11-09-2011, 04:34 AM

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, 08:07 AM

Bowtie2?
Novoalign?

zee · 11-09-2011, 11:26 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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11-09-2011, 04:34 AM	#1
NicoBxl not just another member Location: Belgium Join Date: Aug 2010 Posts: 264	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.

11-09-2011, 08:07 AM	#2
Nicolas Member Location: new york city Join Date: Apr 2009 Posts: 40	Bowtie2? Novoalign?

11-09-2011, 11:26 AM	#3
zee NGS specialist Location: Malaysia Join Date: Apr 2008 Posts: 249	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.