SSPACE

SSPACE scaffolds pre-assembled contigs using paired-read sequencing data to improve the continuity of de novo genome assemblies.

Key Features:

• Stand-alone functionality: Operates independently of de novo assemblers, enabling scaffolding after contig assembly.
• Efficient runtime: Optimized for speed to minimize scaffolding runtime within assembly workflows.
• Multiple library input support: Accepts and integrates multiple paired-end and mate-pair sequencing libraries simultaneously.
• Contig extension capability: Extends contigs by incorporating unmapped sequence reads to increase assembly length and continuity.

Scientific Applications:

• NGS short-read assembly scaffolding: Uses paired-read information to order, orient, and estimate distances between contigs derived from next-generation sequencing data.
• Improving assembly contiguity: Constructs scaffolds that substantially reduce contig counts, demonstrated as at least a 75% reduction in both prokaryotic and eukaryotic test sets.

Methodology:

Determines order, distance and orientation between contigs from paired-read data, integrates multiple paired-end and mate-pair libraries, and extends contigs using unmapped sequence reads.