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Alternative name: A5-miseq

Produces assemblies of quality comparable to a leading assembly algorithm, SOAPdenovo, without any prior knowledge of the particular genome being assembled. A5 is an assembly pipeline that simplifies the entire genome assembly process by automating these stages, by integrating several previously published algorithms with new algorithms for quality control and automated assembly parameter selection. A5 has modest compute requirements, and can assemble a typical bacterial genome on current desktop or laptop computer hardware in under two hours, depending on depth of coverage.

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A5 classification

A5 specifications

Software type:
Restrictions to use:
Operating system:
Unix/Linux, Mac OS
Computer skills:
Command line interface
Biological technology:
GNU General Public License version 2.0

A5 distribution


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A5 support



  • Aaron E. Darling <>
  • Aaron E. Darling <>


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Genome Center, University of California Davis, Davis, CA, USA; Department of Evolution and Ecology, University of California Davis, Davis, CA, USA; Department of Medical Microbiology and Immunology, University of California Davis, Davis, CA, USA; Department of Biomedical Engineering, University of California Davis, Davis, CA, USA

Funding source(s)

This work was supported by National Science Foundation award ER 0949453.

Link to literature

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