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Repeat-aware evaluation of scaffolding tools

Mandric, Igor, Knyazev, Sergey, Zelikovsky, Alex
Bioinformatics 2018 v.34 no.15 pp. 2530-2537
algorithms, bioinformatics, data collection, genome, genome assembly, nucleotide sequences
Genomic sequences are assembled into a variable, but large number of contigs that should be scaffolded (ordered and oriented) for facilitating comparative or functional analysis. Finding scaffolding is computationally challenging due to misassemblies, inconsistent coverage across the genome and long repeats. An accurate assessment of scaffolding tools should take into account multiple locations of the same contig on the reference scaffolding rather than matching a repeat to a single best location. This makes mapping of inferred scaffoldings onto the reference a computationally challenging problem. This paper formulates the repeat-aware scaffolding evaluation problem, which is to find a mapping of the inferred scaffolding onto the reference maximizing number of correct links and proposes a scalable algorithm capable of handling large whole-genome datasets. Our novel scaffolding validation framework has been applied to assess the most of state-of-the-art scaffolding tools on the representative subset of Genome Assembly Golden-Standard Evaluations (GAGE) datasets and some novel simulated datasets. The source code of this evaluation framework is available at The documentation is hosted at Supplementary data are available at Bioinformatics online.