SSAKE 3.8.2 (Apr 25, 2014)

SSAKE

This release includes an option (-j) for adjusting the kmer length when running SSAKE in TASR mode (-s). A recent Illumina MiSeq dataset is available for testing SSAKE's performance: ftp://ftp.bcgsc.ca/supplementary/SSAKE

For additional information about this project, please visit the overview page .

Available downloads

ssake_v3-8-2.tar.gz

For all platforms (2.3 MB)

Release Notes

State Final release
License GPL
Release Manager Rene Warren

SSAKE v3.8.2 no longer constrains the use of 15-character words derived from a target/seed (-s) sequence for interrogating candidate reads. User-defined target kmer length values are now passed to the algorithm using the -j option (equivalent to -k in TASR). Using larger -j values should help speed up the search when using long sequence reads, since it will restrict the sequence space accordingly. Note: whereas specificity, speed and RAM usage may increase with -j, it may yield more sparse/fragmented assemblies. Proper experimentation with various -j values are warranted.

 

*An experimental, quality-trimmed, Illumina MiSeq sequence dataset (PE150, C.showae CC57C [PRJNA189774]) is available for testing SSAKE at: ftp://ftp.bcgsc.ca/supplementary/SSAKE

Project Resources

Project owner: Rene Warren