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Software: SSAKE supports paired-end read data to build scaffolds
Submitted by Rene Warren; posted on Friday, December 21, 2007
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.
SSAKE v3.0 was developed using the previous point release, v2.0.
New functions that use paired-end short read data to build scaffolds were implemented. SSAKE v3.0 tracks all paired reads in the assembly and outputs stats on pairing validity that can be used to identify putative misassemblies.
SSAKE 3.0 is available here: http://www.bcgsc.ca/platform/bioinfo/software/ssake/releases/3.0
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