Package: jellyfish (2.3.1-3 and others)

[ 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: libc6 (>= 2.34) [not ia64]

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

• dep: libc6.1 (>= 2.31) [ia64]

  GNU C könyvtár: megosztott könyvtárak
  also a virtual package provided by libc6.1-udeb

• dep: libgcc-s1 (>= 3.0) [not hppa, ia64, riscv64]

  GCC támogató programkönyvtár

  dep: libgcc-s1 (>= 3.4) [riscv64]

  dep: libgcc-s1 (>= 4.2) [ia64]

• dep: libgcc-s4 (>= 4.1.1) [hppa]

  GCC támogató programkönyvtár

• dep: libhts3 (>= 1.10) [ia64]

  C library for high-throughput sequencing data formats

  dep: libhts3 (>= 1.17) [hppa]

• dep: libhts3t64 (>= 1.17) [not hppa, ia64]

  C library for high-throughput sequencing data formats

• dep: libjellyfish-2.0-2 (= 2.3.0-12) [ia64]

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

  dep: libjellyfish-2.0-2 (= 2.3.1-2+b1) [hppa]

  dep: libjellyfish-2.0-2 (= 2.3.1-3+b3) [amd64, arm64]

  dep: libjellyfish-2.0-2 (= 2.3.1-3+b4) [mips64el, ppc64el, riscv64]

• dep: libstdc++6 (>= 13.1) [not ia64]

  GNU Standard C++ Library v3

  dep: libstdc++6 (>= 9) [ia64]

• dep: libunwind8 [ia64]

  library to determine the call-chain of a program - runtime

Download jellyfish

Download for all available architectures

Architecture	Version	Package Size	Installed Size	Files
amd64	2.3.1-3+b3	776.4 kB	2,471.0 kB	[list of files]
arm64	2.3.1-3+b3	695.4 kB	2,447.0 kB	[list of files]
hppa (unofficial port)	2.3.1-2+b1	682.7 kB	2,079.0 kB	[list of files]
ia64 (unofficial port)	2.3.0-12	847.7 kB	5,022.0 kB	[list of files]
mips64el	2.3.1-3+b4	654.5 kB	3,084.0 kB	[list of files]
ppc64el	2.3.1-3+b4	734.7 kB	2,895.0 kB	[list of files]
riscv64	2.3.1-3+b4	745.3 kB	1,947.0 kB	[list of files]