Jellyfish

Jellyfish/Jellyfish2

 

Jellyfish and Jellyfish2 are tools for fast, memory-efficient counting of k-mers in DNA. Some inmportant differences between the two are:

• In Jellyfish, the is a limit to the size of k-mers (k<=31); there is no limit in Jellyfish2
• Support for Quake has been dropped in Jellyfish2; use Jellyfish with Quake 

See the Jellyfish2 User Guide for more information on the differences.

Documentation

 

• Jellyfish web home
• Jellyfish2 web home
• Citation: If you use Jellyfish in your research, please cite:
  • Guillaume Marcais and Carl Kingsford, A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics (2011) 27(6): 764-770 doi:10.1093/bioinformatics/btr011

 

Usage

To see what versions of Jellyfish are available type

module avail jellyfish

To see what other modules are needed, what commands are available and how to get additional help type one of these commands:

module help jellyfish
module help jellyfish2

To use Jellyfish or Jellyfish2, include a command like one of these in your batch script or interactive session to load the correct module:

module load jellyfish
module load jellyfish2

Be sure you also load any other modules needed, as listed by the module help jellyfish  or module help jellyfish2 command.