Bug#871501: ITP: jellyfish1 -- count k-mers in DNA sequences
Package: wnpp
Severity: wishlist
Owner: Andreas Tille <tille@debian.org>
* Package name : jellyfish1
Version : 1.1.11
Upstream Author : Guillaume Marçais1, Carl Kingsford
* URL : http://www.cbcb.umd.edu/software/jellyfish/
* License : BSD-like
Programming Lang: C++
Description : 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.
Remark: Jellyfish1 is no new package. It used to be in Debian but
the code migrated to version 2 which is not compatible with all our
tools. So there is a need to keep the latest release of version 1.x
which is packaged here. The package is maintained by the Debian
Med team at
https://anonscm.debian.org/git/debian-med/jellyfish1.git
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