With next generation sequencing technologies producing vast amounts of nucleotide data, it becomes imperative to streamline and automate the genome assembly process as much as possible. Contig scaffolding algorithms, ideally designed to reconstruct full chromosomes, more often tend to produce a still intractable number of disjoint sequences, requiring further manual finishing of the genome. To this end we present ScaffoldScaffolder, an aggressive automated scaffold finisher which further reduces the scaffold set using paired-end data. We evaluate the performance of ScaffoldScaffolder on Newbler scaffolds created from the Rubus idaeus cultivar heritage raspberry species. Further automated genome finishing methods are discussed.
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