Provides a de novo assembler for short DNA sequence reads. SSAKE is designed to help leverage the information from short sequences reads by assembling them into contigs and scaffolds that can be used to characterize novel sequencing targets. SSAKE assembles whole reads (not k-mers) and as such, is well-suited for structural variant assembly/detection. SSAKE is written in PERL and runs on Linux. SSAKE cycles through short sequence reads stored in a hash table and progressively searches through a prefix tree for extension candidates. The algorithm assembled 25 to 300 bp (genome, transcriptome, amplicon) reads from viral, bacterial and fungal genomes. SSAKE is lightweight, simple to setup & run and robust.
