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--- archive:bioinformatic_tools:ssake [2010/04/13 16:22]
learithe created
+++ archive:bioinformatic_tools:ssake [2015/07/28 06:27] (current)
ceisenhart ↷ Page moved from bioinformatic_tools:ssake to archive:bioinformatic_tools:ssake
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 ====== SSAKE ======
-The original paper describing SSAKE: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/4/500
+==== 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>

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