Using Bowtie Not Bowtie2


I want to use Bowtie not Bowtie2. So i saw a tool named(Map with bowtie with illumina). is that the same bowtie ?

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Yes, the tool Map with Bowtie for Illumina is a wrapper for bowtie 1, not 2.

Bowtie2, the one you don’t want, is Bowtie2 - map reads against reference genome.