A de novo assembler for single molecule sequencing reads, such as PacBio and Oxford Nanopore

Flye Plugin

Flye is a de novo assembler designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. Flye also includes a special mode for metagenome assembly.

Quick Start

Install the plugin by downloading the gplugin file and dragging it in to Geneious Prime 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 - De Novo Assemble in the toolbar. Flye is available as an option in the Algorithm drop-down menu.


1.3.1 (17 Oct 2023) – Download for Geneious 2020.1

– Use bundled python interpreter on MacOS to avoid relying on system python

1.3.0 (19 Sep 2022) – Download for Geneious 2021.1

– Fixes crash with python 3.8 on Mac

1.2.0 (02 May 2022) – Download for Geneious 2020.1

– Fixed issue with Flye not working with latest versions of MacOS

1.1.0 (10 Mar 2020) – Download for Geneious 2020.1

– Upgraded from Flye 2.6 to Flye 2.7 (which produces better results, has a PacBio HiFi mode, and an option to retain alternative haplotypes)

1.0.0 (11 Feb 2020) – Download for Geneious 2020.1


Mikhail Kolmogorov, Jeffrey Yuan, Yu Lin and Pavel Pevzner, "Assembly of Long Error-Prone Reads Using Repeat Graphs", Nature Biotechnology, 2019 doi:10.1038/s41587-019-0072-8

Yu Lin, Jeffrey Yuan, Mikhail Kolmogorov, Max W Shen, Mark Chaisson and Pavel Pevzner, "Assembly of Long Error-Prone Reads Using de Bruijn Graphs", PNAS, 2016 doi:10.1073/pnas.1604560113


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