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Updated: Apr 21, 2026

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies
Published on: August 20, 2021
A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data
David Coil1, Guillaume Jospin1, Aaron E Darling1
1Genome Center, University of California Davis, Davis, CA 95616, USA and ithree institute, University of Technology Sydney, New South Wales, Australia.
Motivation:
Open-source bacterial genome assembly remains inaccessible to many biologists because of its complexity. Few software solutions exist that are capable of automating all steps in the process of de novo genome assembly from Illumina data.
Results:
A5-miseq can produce high-quality microbial genome assemblies on a laptop computer without any parameter tuning. A5-miseq does this by automating the process of adapter trimming, quality filtering, error correction, contig and scaffold generation and detection of misassemblies. Unlike the original A5 pipeline, A5-miseq can use long reads from the Illumina MiSeq, use read pairing information during contig generation and includes several improvements to read trimming. Together, these changes result in substantially improved assemblies that recover a more complete set of reference genes than previous methods.
Availability:
A5-miseq is licensed under the GPL open-source license. Source code and precompiled binaries for Mac OS X 10.6+ and Linux 2.6.15+ are available from http://sourceforge.net/projects/ngopt
Contact:
aaron.darling@uts.edu.au
Supplementary Information:
Supplementary data are available at Bioinformatics online.
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