Merge paired sequencing reads using FLASH

Requires Geneious 8.1+

  • Experimental
FLASH (Fast Length Adjustment of SHort reads) is a very fast and accurate software tool to merge paired-end reads from next-generation sequencing experiments. FLASH is designed to merge pairs of reads when the original DNA fragments are shorter than twice the length of reads. The resulting longer reads can significantly improve genome assemblies. They can also improve transcriptome assembly when FLASH is used to merge RNA-seq data.

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.