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ssake

genomics application for assembling millions of very short DNA sequences

The Short Sequence Assembly by K-mer search and 3′ read Extension (SSAKE) is a genomics application for aggressively assembling millions of short nucleotide sequences by progressively searching for perfect 3′-most k-mers using a DNA prefix tree. SSAKE is designed to help leverage the information from short sequences reads by stringently clustering them into contigs that can be used to characterize novel sequencing targets.
Homepage:
Package version:3.5-1
Architecture:all
Distribution:Debian
Filename:ssake_3.5-1_all.deb

/usr/share/doc/ssake/README.Debian

SSAKE for Debian
================

The original ssake tarball contains a directory tools which contains
some older versions of ssake as well as

    makeFastaFileFromScaffolds.pl
    nLength.pl

The use of these scripts has to be clarified.  For the moment these
are installed into /usr/share/ssake. If you need these tools at a more
prominent place kust send an e-mail to the Debian package author (
more»

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

SSAKE(1)                                                    SSAKE(1)



NAME
       ssake - assembling millions of very short DNA sequences


SYNOPSIS
       Progressive assembly of millions of short DNA sequences by k-
       mer search through a prefix tree and 3' extension.


OPTIONS
       -f     Fasta  file  containing  all  the  [paired  (-p  1)  /
              unpaired  (-p  0)]  reads (re
more»

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

TQS(1)                                                        TQS(1)



NAME
       tqs - Trim Quality Solexa-Illumina Sequences


SYNOPSIS
       Quality  trim  solexa-Illumina  sequence  reads  using  user-
       defined thresholds.


OPTIONS
       -h, --help
                 show this help message and exit

       -f SEQFILE, --sequence file=SEQFILE
                 Illumina sequence file - O
more»

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

ssake (3.5-1) unstable; urgency=low

  * New upstream version
  * debian/source/format: Switched to 
more»

/usr/share/doc/ssake/copyright

Machine-readable license summary, see ‘http://dep.debian.net/deps/dep5/’.

Name: SSAKE
Contact: 
more»

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