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jellyfish (version 2.3.0+galaxy1)

Jellyfish command: :

Input data file:

Length of mer:

Initial hash size in Million (M):

Counter Length in bits:

Count both strand and canonical representation:

Use bloom filters:

Count only k-mers in this file:

Maximum number of repropbes:

Dump in text format:

Lower count:

Don't output k-mer with count less than this value

upper count:

Don't output k-mer with count greater than this value

Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence. Jellyfish can count k-mers using an order of magnitude less memory and an order of magnitude faster than other k-mer counting packages by using an efficient encoding of a hash table and by exploiting the "compare-and-swap" CPU instruction to increase parallelism.

JELLYFISH is a command-line program that reads FASTA and multi-FASTA files containing DNA sequences. It outputs its k-mer counts in a binary format, which can be translated into a human-readable text format using the "jellyfish dump" command, or queried for specific k-mers with "jellyfish query". See the documentation for details.