General Information
| Description | Using (homologous) proteins to scaffold genomes |
| Homepage | http://www.fishbrowser.org/software/PEP_scaffolder/ |
Publications
PEP_scaffolder: using (homologous) proteins to scaffold genomes
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 contigs; 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.
Availability and Implementation:
The software is freely available at http://www.fishbrowser.org/software/PEP_scaffolder/
Contact:
lijt@cafs.ac.cn
Supplementary information:
Supplementary data are available at Bioinformatics online.
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A generic algorithm for scaffolding next-generation sequencing assemblies
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