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====== 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 : <code>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. </code> ==== Installation ==== SSAKE comes precompiled without source. <code> 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 </code>
