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The de novo assembly of short-read sequencing data usually leads to a fragmented set of genomic sequences (contigs). Ordering and orientating such contigs (scaffolding) represents the first, nontrivial step towards genome finishing and usually requires extensive processing and manual editing of large blocks of sequence (Barton and Barton, 2012). The preferred approach to genome scaffolding is currently based on assembling the sequenced reads into contigs and then using paired-end information to join them into scaffolds. Source text: Bosi et al., 2015.