Reference mapping with Bowtie

Download plugin
Requires Geneious 7.0+

    Bowtie is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. The plugin includes both bowtie2 which runs on all supported operating systems and bowtie which runs only on Linux.

    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.

    7.2.1 (23 May 2017) – Download

    – 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