Overview of the SSPACE-LongRead scaffolding algorithm. A) The input consists of a set of pre-assembled contigs (or scaffolds) in FASTA format and a set of PacBio CLR reads (in FASTA or FASTQ format). B) The PacBio CLR reads are aligned against the contigs using BLASR and only the best alignment matches are kept. In red a repeated element is indicated. C) Contig pairings and multi-contig linkage information is stored, from this information also repeated elements are detected. D) Based on the pairing and linkage information, contigs are ordered, oriented and connected into scaffolds. E) A post-processing step performs the final linearization and circularization.