Can maker be used to improve genome assembly?

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Can maker be used to improve genome assembly?

Emmanuel Nnadi
Hi Carson,
Greetings! This is just a random question that came to my mind. Looking at the way maker structures files and brings contigs together based on "gene" locations. Can this be explored to improve genome assemblies? Maybe a tool that can work from a good annotation to generating a set of improved genome assembly based on these gene locations


Just a thought
Nnaemeka Emmanuel Nnadi,Ph.D
Department of Microbiology,
Faculty of Natural and Applied Science,
Plateau State University, Bokkos, Plateau State, Nigeria.
+2348068124819
Publications: 

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Re: Can maker be used to improve genome assembly?

Carson Holt-2
We haven’t explored this.  On re-assembly projects I rarely find more than a handful of instances where a gene was obviously split across contigs in the first assembly's annotation.  More often what I find is that extra contigs tend to contain fragments of a gene that is complete on another contig in the same assembly (caused by high heterozygosity, so maternal and paternal contigs can assemble independently).

—Carson


On Oct 23, 2020, at 12:15 AM, Emmanuel Nnadi <[hidden email]> wrote:

Hi Carson,
Greetings! This is just a random question that came to my mind. Looking at the way maker structures files and brings contigs together based on "gene" locations. Can this be explored to improve genome assemblies? Maybe a tool that can work from a good annotation to generating a set of improved genome assembly based on these gene locations


Just a thought
Nnaemeka Emmanuel Nnadi,Ph.D
Department of Microbiology,
Faculty of Natural and Applied Science,
Plateau State University, Bokkos, Plateau State, Nigeria.
+2348068124819
Publications: 


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maker-devel mailing list
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http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org

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