SSPACE-LongRead is a stand-alone program for scaffolding pre-assembled contigs using long reads (e.g. PacBio RS reads). Using the long read information, contigs (or scaffolds) are placed in the right order and orientation in so-called super-scaffolds. The SSPACE-LongRead hybrid assembly approach has been tested on a number of bacterial genomes and in most cases results in less than 10 super-scaffolds (numbers based on draft assemblies constructed with one Illumina MiSeq paired-end and one PacBio RS C2 SMRT library, both at 100X coverage).
The manuscript has been published in BMC Bioinformatics. For citations refer to:
- Boetzer M, Pirovano W (2014) SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information. BMC Bioinformatics, 15:211.