Efficient and accurate sequence assembly with MIRA

MIRA Plugin

The MIRA (Mimicking Intelligent Read Assembly) genome fragment assembler is great for "tricky" projects with high numbers of repeats and it can handle hybrid data. MIRA is used for tasks such as mutation detection in different cell types, similarity analysis of transcripts between organisms, and pristine assembly of sequences from various sources for oligo design in clinical microarray experiments. It works best on sequences with up to 100-150 megabases or 20-40 million reads.

Quick Start

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 sequencing reads and clicking on Align/Assemble - De Novo Assemble in the toolbar. MIRA is available under the Algorithm drop-down option.


1.1.2 (02 May 2022) – Download for Geneious 2020.0

– Fixes incompatible locale settings preventing MIRA from running on Ubuntu out of the box

1.1.1 (23 Feb 2017) – Download

– Release open source version of plugin

– Nicer failure message when trying to run MIRA on sequences without quality

– Make compatible with Geneious 10.1 and newer


Chevreux et al. (2004) Using the miraEST Assembler for Reliable and Automated mRNA Transcript Assembly and SNP Detection in Sequenced ESTs, Genome Research 2004. 14:1147-1159.


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