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jonas-fuchs authored Dec 21, 2022
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## Genome visualisation

Creates a genome map based on [gff3 files](https://github.com/jonas-fuchs/SARS-CoV-2-analyses/tree/main/Genome%20visualisation/sequence.gff3) and annotes variants from SNPeff annotated [vcf files](https://github.com/jonas-fuchs/SARS-CoV-2-analyses/tree/main/Genome%20visualisation/test.vcf). Comparison to [reference vcfs](https://github.com/jonas-fuchs/SARS-CoV-2-analyses/tree/main/Genome%20visualisation/ref.vcf) is possible (difference/union).
Creates a publication ready genome map based on [gff3 files](https://github.com/jonas-fuchs/SARS-CoV-2-analyses/tree/main/Genome%20visualisation/sequence.gff3) and shows variants from SNPeff annotated [vcf files](https://github.com/jonas-fuchs/SARS-CoV-2-analyses/tree/main/Genome%20visualisation/test.vcf). Comparison to [reference vcfs](https://github.com/jonas-fuchs/SARS-CoV-2-analyses/tree/main/Genome%20visualisation/ref.vcf) is possible (difference/union).

```R
Genome visualisation/genome_vis.R
```

Multiple options let you explore the genome in more detail:
Multiple options let you explore the genome in more detail and customize the final plots:

![Example output](https://raw.githubusercontent.com/jonas-fuchs/SARS-CoV-2-analyses/main/Genome%20visualisation/gif.gif)

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