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conmeehan committed Oct 3, 2023
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## Worksheets
### UNIX shell approaches
[SPAdes for bacterial and viral genome assembly (short reads)](https://conmeehan.github.io/PathogenDataCourse/Worksheets/GenomeAssembly_SPAdes)
[Flye for bacterial and viral genome assembly (Long reads)](https://conmeehan.github.io/PathogenDataCourse/Worksheets/GenomeAssembly_Flye)
[BUSCO and Bandage for genome completeness and quality checking](https://conmeehan.github.io/PathogenDataCourse/Worksheets/GenomeQC_BUSCO_Bandage)
[Bakta for genome annotation](https://conmeehan.github.io/PathogenDataCourse/Worksheets/GenomeAnnotation_Bakta)
[Snippy for reference mapping (SNP calling)](https://conmeehan.github.io/PathogenDataCourse/Worksheets/GenomeMapping_Snippy)
* [SPAdes for bacterial and viral genome assembly (short reads)](https://conmeehan.github.io/PathogenDataCourse/Worksheets/GenomeAssembly_SPAdes)
* [Flye for bacterial and viral genome assembly (Long reads)](https://conmeehan.github.io/PathogenDataCourse/Worksheets/GenomeAssembly_Flye)
* [BUSCO and Bandage for genome completeness and quality checking](https://conmeehan.github.io/PathogenDataCourse/Worksheets/GenomeQC_BUSCO_Bandage)
* [Bakta for genome annotation](https://conmeehan.github.io/PathogenDataCourse/Worksheets/GenomeAnnotation_Bakta)
* [Snippy for reference mapping (SNP calling)](https://conmeehan.github.io/PathogenDataCourse/Worksheets/GenomeMapping_Snippy)

### Galaxy approaches
* [Bacterial genome assembly using Galaxy](https://training.galaxyproject.org/training-material/topics/assembly/)
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