2015-07-30Zeitschriftenartikel DOI: 10.1186/s12859-015-0644-7
SuRankCo: supervised ranking of contigs in de novo assemblies
Dabrowski, Piotr Wojtek
Piro, Vitor C.
Renard, Bernhard Y.
Background: Evaluating the quality and reliability of a de novo assembly and of single contigs in particular is challenging since commonly a ground truth is not readily available and numerous factors may influence results. Currently available procedures provide assembly scores but lack a comparative quality ranking of contigs within an assembly. Results: We present SuRankCo, which relies on a machine learning approach to predict quality scores for contigs and to enable the ranking of contigs within an assembly. The result is a sorted contig set which allows selective contig usage in downstream analysis. Benchmarking on datasets with known ground truth shows promising sensitivity and specificity and favorable comparison to existing methodology. Conclusions: SuRankCo analyzes the reliability of de novo assemblies on the contig level and thereby allows quality control and ranking prior to further downstream and validation experiments.
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