I am interested in segmental duplications detection after de novo genome assembly. After review several papers, there are some softwares could be annotated segmental duplications, and they were rely on previously library, or need next-generation sequencing data.
It seemed only whole-genome analysis comparison pipeline (WGAC), whole-genome sequence detection (WSSD) developed by the lab of Eichler could be used (Segmental duplications: organization and impact within the current human genome project assembly and Recent segmental duplications in the human genome). However, I couldn't find relative software. Although I can try to finished the pipeline by writing scripts, some steps such as blast_end_trim may be out of my ability. So I wonder whether there are other tools for segmental duplications, or could the WGAC and WSSD available from any website?
Any suggestion would be grateful!