Jellyfish 2.1.1

Jellyfish is a fast, parallel k-mer counter for DNA.

Module file

The module file can be found in this location:

 /cm/shared/modulefiles/SHARED/

<source lang='tcl'>

1. %Module1.0#######################################################################
   1. Jellyfish 2.1.1 modulefile

proc ModulesHelp { } {

       puts stderr "\tAdds Jellyfish 2.1.1 to your environment"

}

module-whatis "Adds Jellyfish 2.1.1 to your environment"

set jellyfish_211_bin /cm/shared/apps/SHARED/jellyfish/jellyfish-2.1.1/bin/bin set jellyfish_211_ldpath /cm/shared/apps/SHARED/jellyfish/jellyfish-2.1.1/bin/lib set jellyfish_211_man /cm/shared/apps/SHARED/jellyfish/jellyfish-2.1.1/bin/share/man set jellyfish_211_pkg /cm/shared/apps/SHARED/jellyfish/jellyfish-2.1.1/bin/lib/pkgconfig

prepend-path PATH $jellyfish_211_bin prepend-path LD_LIBRARY_PATH $jellyfish_211_ldpath prepend-path MANPATH $jellyfish_211_man prepend-path PKG_CONFIG_PATH $jellyfish_211_pkg

</source>

Installation details

Compiled from source using the stock gcc 4.4 of Scientific Linux on 15-03-2014:

  http://www.genome.umd.edu/jellyfish.html

This included the GapCloser software (v1.12), ErrorCorrection (v0.04), and SOAPec (v2.01, includes Corrector_AR, Corrector_HA, KmerFreq_AR and KmerFreq_HA binaries).

See also

• Globally installed software
• ABGC specific modules

External links

• SOAPdenovo2 home page