title: A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data.
abstract: BACKGROUND
  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.
  
  
  BACKGROUND
  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
  
  
  BACKGROUND
  aaron.darling@uts.edu.au
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Genome Center, University of California Davis, Davis, CA 95616, USA and ithree institute, University of Technology Sydney, New South Wales, Australia.
authors.forename: David
authors.initials: D
authors.lastname: Coil
authors.affiliation: Genome Center, University of California Davis, Davis, CA 95616, USA and ithree institute, University of Technology Sydney, New South Wales, Australia.
authors.forename: Guillaume
authors.initials: G
authors.lastname: Jospin
authors.affiliation: Genome Center, University of California Davis, Davis, CA 95616, USA and ithree institute, University of Technology Sydney, New South Wales, Australia.
authors.forename: Aaron E
authors.initials: AE
authors.lastname: Darling
mesh_terms: D000465:Algorithms; D016680:Genome, Bacterial; D023281:Genomics / Q000379:methods*; D011381:Programming Languages; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software