A self optimized base caller for Illumina/Solexa Genome Analyzer (patent pending)

  • Alta-Cyclic is composed of several perl scripts and C programs
  • It requires an SGE cluster environment
  • All dependencies are open source and are downloadable

The following programs and modules should be installed on each node of the computer cluster (except of gcc and gsl). The programs in 'External Programs' section should be in the user path. The Perl modules can be downloaded from CPAN .

External Programs:
NameTested versionLinkDebian/Ubuntu package
4.sun grid engine (SGE)6
6.libSVM-tools libsvm-tools

C libraries:
NameTested versionLinkDebian/Ubuntu package
1.gsl32 libgsl0-dev

Perl Modules:
NameLinkDebian/Ubuntu package
2.PDL pdl
3. PDL::Complex pdl
4.PDL::FFT pdl
6.Getopt::LongMUST BE VERSION 2.35 or newer

  1. Make sure that all programs and modules in the requirment section are installed and accessible from the user path. Notice, these programs should be installed in each node of the cluster.

  2. Download Alta-Cyclic package.

  3. Untar Alta-Cyclic package and copy it to any folder in your submission node.

  4. Go to:
    and compile SVD.c by:
    gcc $(gsl-config --cflags) SVD.c $(gsl-config --libs) -o svd

  5. You are ready to go! (See FAQ for more questions and issues).