Package: jellyfish1 (1.1.11-9 and others)

[ Source: jellyfish1  ]

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

• dep: libc6 (>= 2.33) [ppc64, sparc64, x32]

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

  dep: libc6 (>= 2.34) [amd64, hppa, mips64el, ppc64el, riscv64]

  dep: libc6 (>= 2.38) [arm64]

• dep: libc6.1 (>= 2.33) [alpha]

  GNU C Library: Shared libraries
  also a virtual package provided by libc6.1-udeb

  dep: libc6.1 (>= 2.37) [ia64]

• dep: libgcc-s1 (>= 3.0) [not alpha, hppa, ia64, riscv64, sparc64]

  GCC support library

  dep: libgcc-s1 (>= 3.4) [alpha, riscv64, sparc64]

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

• dep: libgcc-s4 (>= 4.1.1) [hppa]

  GCC support library

• dep: libstdc++6 (>= 11) [alpha, ppc64, sparc64, x32]

  GNU Standard C++ Library v3

  dep: libstdc++6 (>= 13.1) [not alpha, ppc64, sparc64, x32]

• dep: libunwind8 [ia64]

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

• enh: kraken

  assigning taxonomic labels to short DNA sequences

Download jellyfish1

Download for all available architectures

Architecture	Version	Package Size	Installed Size	Files
alpha (unofficial port)	1.1.11-7	134.2 kB	719.0 kB	[list of files]
amd64	1.1.11-9	129.2 kB	651.0 kB	[list of files]
arm64	1.1.11-9+b1	129.8 kB	684.0 kB	[list of files]
hppa (unofficial port)	1.1.11-9	148.8 kB	673.0 kB	[list of files]
ia64 (unofficial port)	1.1.11-9	148.7 kB	939.0 kB	[list of files]
mips64el	1.1.11-9	114.6 kB	774.0 kB	[list of files]
ppc64 (unofficial port)	1.1.11-7	136.8 kB	748.0 kB	[list of files]
ppc64el	1.1.11-9	137.3 kB	747.0 kB	[list of files]
riscv64	1.1.11-9+b1	122.6 kB	584.0 kB	[list of files]
sparc64 (unofficial port)	1.1.11-7	120.6 kB	644.0 kB	[list of files]
x32 (unofficial port)	1.1.11-7	134.5 kB	615.0 kB	[list of files]