ssake - or The Short Sequence Assembly by K-mer search and 3' read Extension - assembles millions of short nucleotide sequences. It progressively searching for perfect 3'-most k-mers using a DNA prefix tree. ssake cycles through short sequence reads stored in a hash table and progressively searches through a prefix tree for the longest possible identical overlap between any two sequences.

Note:The ssake documentation strongly recommends using the tqs script for quality trimming reads before assembly.

The ssake package is prepared by Debian-med and can be installed on Bio-Linux by typing:

For further details, please see the remote documentation.

Other tools available on Bio-Linux for handling data from new sequencing technologies are described in the bioinformatics documentation on the NEBC website.