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jellyfish: JELLYFISH is a tool for fast, memory-efficient counting of k-mers in DNA.

Overview of package

Package: jellyfish
Description: JELLYFISH is a tool for fast, memory-efficient counting of k-mers in DNA.
For more information: http://genome.umd.edu/jellyfish.html
Categories: Genomics
License: OpenSource (GPLv3)

General Usage

Jellyfish is a command-line tool for fast, memory-efficient counting of k-mers in DNA. It reads FASTA and multi-FASTA files containing DNA sequences and outputs its k-mer counts.

This module will add the jellyfish command to your PATH.

In case you need to link against this library in your code, the following environmental variables have been defined:

  • $JELLYFISH_ROOT has been set to the root of the jellyfish installation
  • $JELLYFISH_LIBDIR points to the directory containing the libraries
  • $JELLYFISH_INCDIR points to the directory containing the header files

You will probably wish to use these by adding the following flags to your compilation command (e.g. to CFLAGS in your Makefile):

  • -I$JELLYFISH_INCDIR

and the following flags to your link command (e.g. LDFLAGS in your Makefile):

  • -L$JELLYFISH_LIBDIR -Wl,-rpath,$JELLYFISH_LIBDIR

Available versions by cluster

This section lists the available versions of the package jellyfishon the UMD HPC clusters.

Versions available on the Zaratan cluster

Version Module tags CPU(s) optimized for GPU ready?
2.2.7 2.2.7 icelake, x86_64, zen, zen2 Yes