Filewatcher File Search File Search
Catalog
Content Search
» » » » »

jellyfish

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.

Homepage:
Package version:1.1.5-1
Architecture:kfreebsd-amd64
Distribution:Debian
Filename:jellyfish_1.1.5-1_kfreebsd-amd64.deb

/usr/share/doc/jellyfish/README

Installation
============

% ./configure
% make
# As root:
% make install

To install in a custom directory:

% ./configure --prefix=/my/dir
% make
% make install

Then make sure the following environment variables contain the correct
paths:

PATH            -> /my/dir/bin
LD_LIBRARY_PATH -> /my/dir/lib
MANPATH         -> /my/dir/share/man
PKG_CONFIG_PATH -> /my/dir/lib/pkgconfig

Only the PATH en
more»

/usr/share/man/man1/jellyfish.1.gz

JELLYFISH(1)               k-mer counter                JELLYFISH(1)



NAME
       jellyfish - count k-mers in DNA sequences

SYNOPSIS
       jellyfish count [-oprefix] [-mmerlength] [-tthreads] [-shash‐
       size] [--both-strands] fasta [fasta ...  ]
       jellyfish merge hash1 hash2 ...
       jellyfish dump hash
       jellyfish stats hash
       jellyfish histo [-hhigh] [-llow] [-iincrem
more»

/usr/share/doc/jellyfish/changelog.Debian.gz

jellyfish (1.1.5-1) unstable; urgency=low

  * New upstream version fixing the FTBFS with gcc-4.7 bug
    Closes: #667214
  * debian/patches/fix-unused-but-set-variable.patch: Removed
    because applied upstream

 -- Andreas Tille <tille@debian.org>  Mon, 21 May 2012 21:56:38 +0200

jellyfish (1.1.4-1) unstable; urgency=low

  * New upstream version
  * debian/patches/ptrdiff_t: Removed because a
more»

/usr/share/doc/jellyfish/copyright

Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: JELLYFISH
U
more»

Browse inside jellyfish_1.1.5-1_kfreebsd-amd64.deb

         [DIR]DEBIAN/ (2)  65535+ mirrors
         [DIR]usr/ (2)  65535+ mirrors

Download jellyfish_1.1.5-1_kfreebsd-amd64.deb

Results 1 - 1 of 1
Help - FTP Sites List - Software Dir.
Search over 15 billion files
© 1997-2016 FileWatcher.com