A versatile mapper / pairwise aligner for genomic and spliced nucleotide sequences

Minimap2 Plugin

Minimap2 is a versatile aligner suited to mapping Oxford Nanopore and PacBio reads to a reference sequence. Its uses include aligning long-read sequences, aligning sequences with error rates up to ~15%, performing splice-aware alignments, and performing alignment between two closely related species with divergence below ~15%.

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 - Map to Reference in the toolbar. Minimap2 is available as an option in the Algorithm drop-down menu.


2.1.0 (02 May 2022) – Download for Geneious 2020.1

– Updates minimap2 to version 2.24

2.0.0 (11 Feb 2020) – Download for Geneious 2020.1

– Added option for specifying whether to produce secondary alignments and options for which conditions to do this in.

1.0.0 (22 Oct 2019) – Download for Geneious 2020


Li, H (2018) Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics, 34(18), 3094–3100


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