jellyfish

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  "desc": "Fast, memory-efficient counting of DNA k-mers",
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  "full_name": "jellyfish",
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  "github_readme_excerpt": "![CI workflow](https://github.com/gmarcais/Jellyfish/actions/workflows/c-cpp.yml/badge.svg)\n\n# Jellyfish\n\n## Overview\n\n\nJellyfish 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.\n\nJELLYFISH is a command-line program that reads FASTA and multi-FASTA files containing DNA sequences. It outputs its k-mer counts in a binary format, which can be translated into a human-readable text format using the \"jellyfish dump\" command, or queried for specific k-mers with \"jellyfish query\". See the [documentation](doc/Readme.md) for details.\n\nIf you use Jellyfish in your research, please cite:\n\n  Guillaume Marcais and Carl Kingsford, A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics (2011) 27(6): 764-770 ([first published online January 7, 2011](http://bioinformatics.oxfordjournals.org/cgi/content/abstract/27/6/764 \"Paper on Oxford Bioinformatics website\")) doi:10.1093/bioinformatics/btr011\n\n## Installation\n\n### Linux Binaries\n\nOn Debian and Ubuntu with `apt`:\n```Shell\nsudo apt update\nsudo apt install jellyfish\n```\n\nOn Arch, it is available from [AUR](https://aur.archlinux.org/packages/jellyfish/).\n\n### FreeBSD\n\nJellyfish can be installed on FreeBSD via the FreeBSD ports system.\n\nTo install via the binary package, simply run:\n```Shell\npkg install Jellyfish\n```\n\nTo install from source:\n```Shell\ncd /usr/ports/biology/jellyfish\nmake install\n```\n\n### Windows\n\nWith [Cygwin](https://www.cygwin.com/), Jellyfish can be compiled from source as [explained below](#from-source).\nThe simpler way on Windows 10 is to first install [WSL](h",
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  "license": "BSD-3-Clause OR GPL-3.0-or-later",
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