Best Aligner for Duplicated Sequences

[luc]

Razer S3 looks appropriate:

http://bioinformatics.oxfordjournals.org/content/28/20/2592.full

[ethanb416]

Thanks bioinfosm! I'll look into that. Do you have any experience with stampy or novoalign?

[bioinfosm]

i think you should change the query to aligner for multiply mapped reads!
most aligners you mention have different options to select multiply mapped reads, so it might end up being multiple options from the same tool as well...

[ethanb416]

I'm looking around for some input from fellow SEQers. I'm experimenting with different aligners. I'm looking for an aligner that does a good job of correctly mapping reads from duplicated sequences, while at the same time is used fairly commonly. I am already looking into bwa, bowtie, and snap, but I would like to add one more to the list. Any suggestions? Would novoalign or stampy be good choices?