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# Introduction

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## [Basty](https://git.lumc.nl/biopet/biopet/tree/develop/protected/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty)

A pipeline for aligning bacterial genomes and detect structural variations on the level of SNPs. Basty will output phylogenetic trees.
Which makes it very easy to look at the variations between certain species.

# Tools
* GATK-pipeline []()
* FASTA builder [BastyGenerateFasta](../tools/BastyGenerateFasta.md)
* RAxml []()
* Gubbins []()

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# Invocation

# Example

# Testcase A

# Testcase B

# Examine results

## Result files

## Best practice

# References