SSPACE (SSAKE-based Scaffolding of Pre-Assembled Contigs after Extension) 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.
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Marten Boetzer, Christiaan V. Henkel, Hans J. Jansen, Derek Butler1 and Walter Pirovano
Scaffolding pre-assembled contigs using SSPACE
Bioinformatics (2011, vol. 27(4), pag. 578-9