Package: jellyfish (2.3.1-2 and others) [debports]

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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: libc6 (>= 2.34)

  GNU C könyvtár: megosztott könyvtárak
  also a virtual package provided by libc6-udeb

• dep: libgcc-s4 (>= 4.1.1)

  GCC támogató programkönyvtár

• dep: libhts3 (>= 1.17)

  C library for high-throughput sequencing data formats

• dep: libjellyfish-2.0-2 (= 2.3.1-2+b1)

  count k-mers in DNA sequences (dynamic library of jellyfish)

• dep: libstdc++6 (>= 13.1)

  GNU Standard C++ Library v3

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Architecture	Version	Package Size	Installed Size	Files
hppa (unofficial port)	2.3.1-2+b1	682.7 kB	2,079.0 kB	[list of files]