SSPACE-standard is a stand-alone program for scaffolding pre-assembled contigs using NGS 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 mate-pair 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 (Illumina/454/Solid FASTA or FASTQ). The final scaffolds are provided in FASTA format.

SSPACE has shown excellent performance on various datasets. The results have been published in the high-impact journal Bioinformatics (2011, vol. 27(4), pg. 578-9), but the method is also frequently cited in other papers. SSPACE has been evaluated with a number of competitors in a study conducted by Hunt et. al from the Sanger Institute. The paper “A comprehensive evaluation of assembly scaffolding tools” (Genome Biology, 2014, 15:R42) demonstrates SSPACE produces high-quality scaffolds and recommend to use our tool. Moreover the software is “extremely simple to install and run” and has a very short running time.


In principal the basic version of SSPACE standard is free for academics, upgrades are available against a small additional fee. Commercial users need in any case to pay for a license, the exact fee depends on the size of the institution (number of employees) and the type of usage (R&D or commercial services). If you are interested in a copy of our software, please fill in your contact details below. Note that our software is distributed on a weekly basis. For general information about licenses, software or other services please contact us at

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