PEP_scaffolder: using (homologous) proteins to scaffold genomes

Bai-Han Zhu, Ying-Nan Song, Wei Xue, Gui-Cai Xu, Jun Xiao, Ming-Yuan Sun, Xiao-Wen Sun, Jiong-Tang Li
2016 Bioinformatics  
Motivation: Recovering the gene structures is one of the important goals of genome assembly. In low-quality assemblies, and even some high-quality assemblies, certain gene regions are still incomplete; thus, novel scaffolding approaches are required to complete gene regions. Results: We developed an efficient and fast genome scaffolding method called PEP_scaffolder, using proteins to scaffold genomes. The pipeline aims to recover protein-coding gene structures. We tested the method on human
more » ... igs; using human UniProt proteins as guides, the improvement on N50 size was 17% increase with an accuracy of 97%. PEP_scaffolder improved the proportion of fully covered proteins among all proteins, which was close to the proportion in the finished genome. The method provided a high accuracy of 91% using orthologs of distant species. Tested on simulated fly contigs, PEP_scaffolder outperformed other scaffolders, with the shortest running time and the highest accuracy.
doi:10.1093/bioinformatics/btw378 pmid:27334475 pmcid:PMC5048069 fatcat:woodmztiefewfhw4qgqrbxlhmy