Reference mapping with Bowtie

Bowtie Plugin

Bowtie is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. The plugin includes both bowtie2 and bowtie. Only 64 bit operating systems are supported. Bowtie2 is released under the GNU General Public License v3, with source code freely available at

Quick Start

Install the plugin by downloading the gplugin file and dragging it in to Geneious or use the plugin manager in Geneious (under Tools - Plugins in the menu).

Once installed, run the plugin by selecting your reads and reference sequence then clicking on Align/Assemble - Map to Reference in the toolbar. Bowtie is available as an option in the Algorithm drop-down menu.


7.2.2 (14 Jul 2022) – Download for Geneious 2020.0

– Improved Bowtie command line parameters help

– Upgraded Bowtie2 to 2.4.5

7.2.1 (23 May 2017) – Download for Geneious 7.0

– Removed the debug executables for Windows which were required for Bowtie2 2.2.6

– Upgraded Bowtie2 to 2.3.0 on Windows, 2.3.2 on Linux and MacOS


For Bowtie2: Langmead B, Salzberg S. Fast gapped-read alignment with Bowtie 2. Nature Methods. 2012, 9:357-359.

For Bowtie: Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25


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