https://github.com/applicativesystem/pangenome-genome-assembly

bash based pangenome assembly from short and long reads
https://github.com/applicativesystem/pangenome-genome-assembly

bioinformatics bioinformatics-data genome-analysis genome-assembly genome-assembly-evaluation pangenome

Last synced: 18 days ago
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bash based pangenome assembly from short and long reads

• Host: GitHub
• URL: https://github.com/applicativesystem/pangenome-genome-assembly
• Owner: applicativesystem
• License: mit
• Created: 2024-08-19T20:41:03.000Z (5 months ago)
• Default Branch: main
• Last Pushed: 2024-09-12T08:03:50.000Z (4 months ago)
• Last Synced: 2024-11-10T20:18:15.728Z (about 2 months ago)
• Topics: bioinformatics, bioinformatics-data, genome-analysis, genome-assembly, genome-assembly-evaluation, pangenome
• Language: Shell
• Homepage:
• Size: 105 KB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# pangraphs-genome-assembly

- This code is constantly updated and also a docker withe several integrations is in preparation which will allow you to run the dockerized analysis. 

- a complete workflow that can be dockerized for the long read assembly, it allows for the genome assembly update as well as it allows for the assembly from the start. if you have the illumina reads it allows for the genome mapping also. 

- 2023-10-20, finished code first release: next update will be with the genome visualization tracts. 

- 2023-10-21, Finished update: major changes to the code, added associative arrays and added the support for the multiple genome polishing such as pilon and jasper and also the coverage analysis 

- 2024-2-20:, adding the support for the pacbiohifi, chromosomal polishing and structural rearrangements.

Gaurav Sablok \

University of Potsdam \

Potsdam,Germany