SSPACE, SSAKE-based Scaffolding of Pre-Assembled Contigs after Extension, is a script able to extend and scaffold pre-assembled contigs using one or more mate pairs or paired-end libraries, or even a combination.

Some parameters are still missing:

  • trimming options (-t)
  • unpaired single (-u)
  • minimal base ratio (-r)



Scaffolding pre-assembled contigs using SSPACE.
M. Boetzer, C.V. Henkel, H.J. Jansen, D. Butler and W. Pirovano.
Bioinformatics (2011) 27 (4): 578-579.