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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.

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1 user review

1 user review

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Ssake is super easy to use and produces accurate results.
It is lightweight and has no dependencies, I highly recommend it. Because it uses coverage info, assemblies are stratified which makes it also suitable for transcriptome and meta genome assemblies. It is not as greedy as most people report, the correct path is chosen no based on longest overlap, but coverage and reads having a matching pairing partner already assembled

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SSAKE classification

SSAKE specifications

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Command line interface
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SSAKE distribution


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SSAKE support


  • Rene Warren <>


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British Columbia Cancer Agency, Genome Sciences Centre, Vancouver, Canada; J. Craig Venter Institute, Rockville, MD, USA

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