FLASH
Merge paired sequencing reads using FLASH
Requires Geneious 8.1+
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 choosing Tools - Merge Paired Reads using FLASH 1.2.9 from the menu.
1.1 (31 Mar 2015) – Download for Geneious 7.1
– Exposed more options
– Added custom command line
– Improved descriptions
FLASH: Fast length adjustment of short reads to improve genome assemblies. T. Magoc and S. Salzberg. Bioinformatics 27:21 (2011), 2957-63.