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[ Source: jellyfish  ]

Package: jellyfish (2.2.10-2)

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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.

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Download jellyfish

Download for all available architectures
Architecture Package Size Installed Size Files
amd64 352.6 kB608.0 kB [list of files]
arm64 336.4 kB571.0 kB [list of files]
kfreebsd-amd64 352.2 kB604.0 kB [list of files]
mips64el 340.3 kB688.0 kB [list of files]
ppc64el 352.3 kB704.0 kB [list of files]
riscv64 (unofficial port) 351.7 kB541.0 kB [list of files]