BBMap

Fast and sensitive aligner for RNA and DNA

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Requires Geneious 9.0+

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BBMap is a fast and sensitive read mapper that handles Illumina, PacBio, 454, and other reads. It is part of the BBTools package by Brian Bushnell. 

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. BBMap is available as an option in the Algorithm drop-down menu.