Hi!
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!
Best wishes!
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lamz138138 •
1 answer
Look at this article and github link inside, https://academic.oup.com/bioinformatics/article/34/17/i706/5093240 Eichler lab has posted WGAC code and a detailed how-to guide at https://github.com/EichlerLab/WGAC
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Duplication detection software tools | Whole-genome sequencing
A segmental duplication is a feature of a genome, not a variant. It is defined as "Duplications of >1000 Bases of Non-RepeatMasked Sequence (>90 percent similar)." (From: http://varianttools.sourceforge.net/Annotation/GenomicSuperDups)
my bad missleaded by the description in the omic site which was
I will delete it
My guess is that you still need to find the synteny block mapping between your case and control groups first. If you don't see a coverage difference at all in any of the synteny blocks between case and control, you might want to reevaluate your endeavour.... I could be wrong, but my understanding is that these kinds of tasks can take forever to run.