  Motivation: Open-source bacterial genome assembly remains inaccessible to
many biologists due to 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 from
as little as 20-fold sequence data coverage 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
