A5-miseq: an updated pipeline to assemble microbial genomes from   Illumina MiSeq data
  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 
David Coil and Guillaume Jospin and Aaron E. Darling
q-bio.QM q-bio.GN