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Document: jellyfish
Title: Jellyfish: A fast k-mer counter
Author: G. Marcais and C. Kingsford
Abstract: Jellyfish is a software to 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.
Section: Science/Biology
Format: pdf
Files: /usr/share/doc/jellyfish/jellyfish.pdf.gz
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