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archive:bioinformatic_tools:ssake

SSAKE

Overview

The original paper describing SSAKE: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/4/500
Available at: http://www.bcgsc.ca/platform/bioinfo/software/ssake

Descriptions from http://www.bcgsc.ca/platform/bioinfo/software/ssake :

SSAKE 2.0: SSAKE can now handle error-rich [short sequence] data sets. 
For each seed sequence or contig being extended, SSAKE looks through the 
entire overlapping k-mer space and generates a consensus sequence from 
overhanging bases - It then extends contigs using that consensus, provided 
the bases it comprises pass user-defined thresholds.

Version 3.4 [Released 2009-04-14] exploits paired-end reads to explore 
possible contig merges within scaffolds and allows users to track read 
position and individual base coverage for reads *fully embedded* within 
contigs. 

Installation

SSAKE comes precompiled without source.

cd /campusdata/BME235/programs/
wget http://www.bcgsc.ca/platform/bioinfo/software/ssake/releases/3.4/ssake_v3-4-tar.gz
tar -xvf ssake_v3-4-tar.gz
rm ssake_v3-4-tar.gz
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archive/bioinformatic_tools/ssake.txt · Last modified: 2015/07/27 23:27 by ceisenhart