Pittsburgh Supercomputing Center 

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Celera WGS Assembler

    Celera Assembler is a de novo whole-genome shotgun (WGS) DNA sequence assembler.

Installed on blacklight.

Other resources that may be helpful include:

    The standard citation is the original paper [Myers et al. (2000) "A Whole-Genome Assembly of Drosophila." Science 287 2196-2204]. More
    recent papers describe modifications for human genome assembly [Istrail et al. 2004; Levy et al. 2007], metagenomics assembly [Venter
    et al. 2004; Rusch et al. 2007], haplotype separation [Levy et al. 2007; Denisov et al. 2008], a Sanger+pyrosequencing hybrid pipeline
    [Goldberg et al. 2006] and native assembly of 454 data [Miller et al. 2008]. There are links to these papers, and more, in the on-line

    Website: http://wgs-assembler.sourceforge.net/

Running Celera WGS Assembler

1) Make Celera WGS Assembler availiable for use
   a) blacklight:
   The Celera WGS Assembler will be made availiable for use through the module command. To load the Celera WGS Assembler
   module enter:

                module load wgs

2) General Usage:

   runCA -d <dir> -p <prefix> [options] <frg> ...
     -d <dir>                         Use <dir> as the working directory.  Required
     -p <prefix>                    Use <prefix> as the output prefix.  Required
     -s <specFile>               Read options from the specifications file
                                          <specfile>. <specfile> can also be one of the
                                          following key words:
                                                  [no]OBT - run with[out] OBT
                                                  noVec   - run with OBT but without Vector
     -version                       Version information
     -help                            This information
     -options                       Describe specFile options, and show default values
     <frg>                           CA formatted fragment file

3) Example:

            runCA -p test -d test $CELERA_WGS_HOME/example/a006.frg.bz2


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