Reference mapping with Bowtie

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Requires Geneious 7.0+

  • Recently Updated

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)

  • Upgraded Bowtie2 to 2.2.9 which fixes failures on some datasets and reduces gplugin file size
  • 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

7.2.0 (10 Feb 2016)

  • Upgrade Bowtie to 1.1.2, Bowtie2 to 2.2.6
  • Fixed problem where Bowtie2 would fail to run on input containing both paired and unpaired reads.
  • Remove 32-bit support from plugin since Bowtie and Bowtie2 no longer support 32-bit
  • Enable use of Bowtie under Windows (which previously ran only Bowtie2)

7.1.0 (11 Feb 2014)

  • Fix problem that having many reference sequences can cause OS error with too many open files
  • Detect duplicate reference sequence names and gracefully handle as error
  • Add option to enable multithreading in the execution of Bowtie and Bowtie2
  • Update executables, Bowtie to version 1.0.0, Bowtie2 to 2.1.0
  • Enabled to run Bowtie on 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