Difference between revisions of "SSPACE"

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* Validated 4/5/2018

Revision as of 17:48, 5 April 2018


sspace website  

SSPACE is a stand-alone program for scaffolding pre-assembled contigs using paired-read data. It is unique in offering the possibility to manually control the scaffolding process. By using the distance information of paired-end and/or matepair data, SSPACE is able to assess the order, distance and orientation of your contigs and combine them into scaffolds. Currently we offer this as a command-line tool in Perl. The input data is given by pre-assembled contig sequences (FASTA) and NGS paired-read data (FASTA or FASTQ). The final scaffolds are provided in FASTA format.

Required Modules


  • sspace

System Variables

  • HPC_{{#uppercase:sspace}}_DIR


If you publish research that uses sspace you have to cite it as follows:

Boetzer M, Henkel CV, Jansen HJ, Butler D, Pirovano W. 2011. Scaffolding pre-assembled contigs using SSPACE. Bioinformatics 27:578–579.


  • Validated 4/5/2018