TheHumanPangenome

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TheHumanPangenome

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A Strategy for Building and Using a Human Reference Pangenome

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# TheHumanPangenome -- Creation of and Toolsets for Human Pangenomic Analysis

![Alt text](https://github.com/NCBI-Hackathons/TheHumanPangenome/blob/master/DS/graph/ds-vis1.png?raw=true "Title")

#### The path of GRCh38 through a graph! For details check the DS folder! 
https://github.com/NCBI-Hackathons/TheHumanPangenome/tree/master/DS

![Alt text](https://github.com/NCBI-Hackathons/TheHumanPangenome/blob/master/Giraffe/images/01.png?raw=true "Title")

#### A Faster, Better Short-Read Mapper with Hit Chaining. Now with more corn! See the Giraffe folder for details!  
https://github.com/NCBI-Hackathons/TheHumanPangenome/tree/master/Giraffe

![Alt text](https://github.com/NCBI-Hackathons/TheHumanPangenome/blob/master/annotation/fig/annotation_easy_case.svg)

#### Most Genome Annotations can be Imported from gff3 (to ggff!) quite easily!  See the annotation folder for details! 
https://github.com/NCBI-Hackathons/TheHumanPangenome/tree/master/annotation

![Alt text](https://github.com/NCBI-Hackathons/TheHumanPangenome/blob/master/RNA/RNA%20project-5.jpg?raw=true "Title")

#### Allele-Specific Expression can be calculated in a lightweight fashion! Grab the workflow in the RNA folder!
https://github.com/NCBI-Hackathons/TheHumanPangenome/tree/master/RNA

![Alt text](https://github.com/NCBI-Hackathons/TheHumanPangenome/blob/master/SV/Screen%20Shot%202019-03-26%20at%205.06.59%20PM.png?raw=true "Title")

#### Calculate Mutations In, Outside of, and at Breakpoints of Structural Variants! See the SV folder for Details!
https://github.com/NCBI-Hackathons/TheHumanPangenome/tree/master/SV/HG002

![Alt text](https://github.com/NCBI-Hackathons/TheHumanPangenome/blob/master/MHC/Screen%20Shot%202019-03-26%20at%205.13.06%20PM.png?raw=true "Title")

#### We Mapped the MHC Region of HG002 to a Graph with Long Reads, Long Reads, 10X and love.  Check out the MHC folder!
https://github.com/NCBI-Hackathons/TheHumanPangenome/tree/master/MHC

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