Local aligner for short reads

[andrej-gnip]

Hi everyone,

I'm looking for an aligner which would be able to do end-to-end as well as local alignment. By end-to-end I mean that the entire read must align to reference, and by local I mean that sequences might be clipped away at the ends of the read. I tried bowtie2, but the local option is little weird. When I use the local option, I get even less hits than when I use the end-to-end option. So does anyone know about a bug in bowtie2 and how to fix it? Or is there any other aligner I can use? Thanks a lot.

[GenoMax]

BBMap can do local alignments.

[westerman]

I doubt if there is a bug in bowtie2. More likely there is some difference in how you set up your two alignments. That said, yes, BBMap does local alignments and even better the author Brian is active on this forum and can give advice.

[dpryan]

You sometimes have to play with bowtie2's local alignment settings to get decent results. Having said that, I'll echo everyone's mention of BBMap. It's quite quick and Brian is pretty quick with help, which is amazingly helpful.

[andrej-gnip]

Well, according to what you all say it seems that using BBMap is the best thing to do. So I'll go with that. Thanks.

[GenoMax]

Do not forget to add "local=t" command line option for local alignments.