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I am using Ion Torrent 200bp sequencing and looking into aligners. Any opinions as to which of the two (bowtie, bowtie2) may be a better choice? Thanks 
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Bowtie cannot tolerate indels, so it should never be used for Ion Torrent alignment. So between those two, Bowtie2 is the only viable choice, though personally I'd recommend BBMap. The best aligner may depend on your experiment type and organism of interest. -
Thank you very much.... I will look into BBMap as I am not familiar with that.
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