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Package: jellyfish1 (1.1.11-6)

count k-mers in DNA sequences

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 an binary format, which can be translated into a human-readable text format using the "jellyfish dump" command.

This is the latest version of the 1.x series of jellyfish which is used by some other applications that are not compatible with version 2.x which is provided inside the jellyfish package.

Other Packages Related to jellyfish1

  • depends
  • recommends
  • suggests
  • dep: libc6 (>= 2.34)
    GNU C Library: Shared libraries
    also a virtual package provided by libc6-udeb
  • dep: libgcc-s1 (>= 3.3.1) [not armhf]
    GCC support library
    dep: libgcc-s1 (>= 3.5) [armhf]
  • dep: libstdc++6 (>= 11)
    GNU Standard C++ Library v3
  • enh: kraken
    assigning taxonomic labels to short DNA sequences

Download jellyfish1

Download for all available architectures
Architecture Package Size Installed Size Files
amd64 161.8 kB592 kB [list of files]
arm64 158.9 kB560 kB [list of files]
armhf 184.0 kB531 kB [list of files]
ppc64el 172.3 kB684 kB [list of files]