PEP_scaffolder is a novel scaffolding tool using (homologous) proteins to scaffold genome fragments. The method is suitable for most genomes. The program could handle the proteins from target species and close species, or de novo predicted proteins from RNA-seq trascriptome. Our method provides a practical alternative to existing mate-pair_based approaches for scaffolding genome sequences in a cost effective way. Furthermore, our method will greatly improve the completeness of gene regions.

If you feel that the software is useful, please cite Zhu BH, Song YN, Xue W, Xu GC, Xiao J, Sun MY, Sun XW, and Li JT. PEP_scaffolder: using (homologous) proteins to scaffold genomes.Bioinformatics. 2016 Jun 22. pii: btw378. [Epub ahead of print]