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

Requires Geneious 2020.1+

    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.

    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