https://github.com/andreaguarracino/referencegraphpangenomedataanalysishackathon2023

Material for the Reference Graph Pangenome Data Analysis Hackathon 2023, November 13-17 in Cape Town, South Africa
https://github.com/andreaguarracino/referencegraphpangenomedataanalysishackathon2023

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Material for the Reference Graph Pangenome Data Analysis Hackathon 2023, November 13-17 in Cape Town, South Africa

• Host: GitHub
• URL: https://github.com/andreaguarracino/referencegraphpangenomedataanalysishackathon2023
• Owner: AndreaGuarracino
• License: mit
• Created: 2023-11-02T01:03:39.000Z (over 1 year ago)
• Default Branch: master
• Last Pushed: 2023-11-17T13:24:55.000Z (over 1 year ago)
• Last Synced: 2025-01-24T16:38:08.511Z (4 months ago)
• Homepage:
• Size: 2.94 MB
• Stars: 3
• Watchers: 3
• Forks: 2
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# Reference Graph Pangenome Data Analysis Hackathon 2023

Material for the **Reference Graph Pangenome Data Analysis Hackathon 2023**, November 13-17 in Cape Town, South Africa.

The event was sponsored by [H3ABioNet](https://www.h3abionet.org/).

## Table of Contents

* [Reference-based pangenome graph building](01_ReferenceBasedPangenomeGraphBuilding.md)

  * [Constructing and viewing your first graphs](01_ReferenceBasedPangenomeGraphBuilding.md#constructing-and-viewing-your-first-graphs)

* [Small pangenome graph building from sequence alignments](02_SmallPangenomeGraphBuildingFromSequenceAlignments.md)

  * [Building HLA pangenome graphs](02_SmallPangenomeGraphBuildingFromSequenceAlignments.md#building-hla-pangenome-graphs)

  * [Building LPA pangenome graphs](02_SmallPangenomeGraphBuildingFromSequenceAlignments.md#building-lpa-pangenome-graphs)

* [Human pangenome graph building from sequence alignments](03_HumanPangenomeGraphBuildingFromSequenceAlignments.md)

  * [Pangenome Sequence Naming](03_HumanPangenomeGraphBuildingFromSequenceAlignments.md#pangenome-sequence-naming)

  * [Sequence partitioning](03_HumanPangenomeGraphBuildingFromSequenceAlignments.md#sequence-partitioning)

  * [Building chromosome-specific pangenome graphs](03_HumanPangenomeGraphBuildingFromSequenceAlignments.md#building-chromosome-specific-pangenome-graphs)

* [Understanding pangenome graphs](04_UnderstandingPangenomeGraphs.md)

  * [MHC locus](04_UnderstandingPangenomeGraphs.md#mhc-locus)

  * [Graph extraction](04_UnderstandingPangenomeGraphs.md#graph-extraction)

  * [Graph untangling](04_UnderstandingPangenomeGraphs.md#graph-untangling)

  * [Annotation injection](04_UnderstandingPangenomeGraphs.md#annotation-injection)

* [Short read mapping and variant calling](05_ShortReadMappingVariantCalling.md)

* [Hacking with our data](06_HackingWithOurData.md)