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:
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.