Background: The development of next-generation sequencing has made it possible to sequence whole genomes\udat a relatively low cost. However, de novo genome assemblies remain challenging due to short read length,\udmissing data, repetitive regions, polymorphisms and sequencing errors. As more and more genomes are\udsequenced, reference-guided assembly approaches can be used to assist the assembly process. However, previous\udmethods mostly focused on the assembly of other genotypes within the same species. We adapted and extended\uda reference-guided de novo assembly approach, which enables the usage of a related reference sequence to guide\udthe genome assembly. In order to compare and evaluate de novo and our reference-guided de novo assembly\udapproaches, we used a simulated data set of a repetitive and heterozygotic plant genome.\udResults: The extended reference-guided de novo assembly approach almost always outperforms the corresponding\udde novo assembly program even when a reference of a different species is used. Similar improvements can be\udobserved in high and low coverage situations. In addition, we show that a single evaluation metric, like the widely\udused N50 length, is not enough to properly rate assemblies as it not always points to the best assembly evaluated\udwith other criteria. Therefore, we used the summed z-scores of 36 different statistics to evaluate the assemblies.\udConclusions: The combination of reference mapping and de novo assembly provides a powerful tool to improve\udgenome reconstruction by integrating information of a related genome. Our extension of the reference-guided de\udnovo assembly approach enables the application of this strategy not only within but also between related species.\udFinally, the evaluation of genome assemblies is often not straight forward, as the truth is not known. Thus one\udshould always use a combination of evaluation metrics, which not only try to assess the continuity but also the\udaccuracy of an assembly.
展开▼
