Package: jellyfish (1.1.5-1)

[ Source: jellyfish  ]

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.

Other Packages Related to jellyfish

• dep: libc0.1 (>= 2.4) [kfreebsd-amd64]

  Embedded GNU C Library: Shared libraries
  also a virtual package provided by libc0.1-udeb

• dep: libc6 (>= 2.4) [amd64]

  Embedded GNU C Library: Shared libraries
  also a virtual package provided by libc6-udeb

• dep: libgcc1 (>= 1:4.1.1)

  GCC stödbibliotek

• dep: libstdc++6 (>= 4.6)

  GNU Standard C++ Library v3

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Architecture	Package Size	Installed Size	Files
amd64	402.2 kB	800.0 kB	[list of files]
kfreebsd-amd64	401.8 kB	768.0 kB	[list of files]