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There is a plethora of programs that can perform some, or most of these steps. These programs include commercial and open-source options, some are very user friendly and some are extremely difficult to use/install. Common assemblers for bacterial genomes include SPAdes \cite{Bankevich_2012}, MIRA \cite{Chevreux_2004}, SGA \cite{Simpson_2010}, Velvet \cite{Zerbino_2008} CLC (CLC Bio), and A5 \cite{Tritt_2012}. Good sources for overviews of genome assemblers and the assembly process include the GAGE project \cite{Salzberg_2012}, the GAGE-B project \cite{Magoc_2013}, and the Assemblathon Project \cite{Earl_2011}.  For this workflow we recommend use of the open source A5 assembly pipeline which automates all of the steps described above with a single command \cite{Tritt\_2012}. A5 is designed to work with raw, demultiplexed Illumina data and a recent version, A5-miseq, has been optimized for longer reads from the MiSeq (Coil et al submitted). \cite{25338718}.  Input reads must be paired, and the files can be separate (forward reads in one file, reverse reads in another) or interleaved. These files should have the .fastq extension. See (http://en.wikipedia.org/wiki/FASTQ_format) for a description of the fastq format. You may need assistance from your sequencing center in locating and accessing these files. You will need one of the two following (per genome): 1) a single .fastq file that contains both forward and reverse reads, or 2) two .fastq files, one with forward reads and one with the corresponding reverse reads. These FastQ files can optionally be gzip compressed (as indicated by the .gz file name extension). Download/Install A5 from   http://sourceforge.net/projects/ngopt/