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Clockwork - pipelines for processing bacteria Illumina data and variant calling

Note: these pipelines were made for the CRyPTIC project, but in principle can be used on any bacteria.

The following help pages are available:

1. Installation - installation instructions for pipeline users.
2. Running pipelines - how to setup the (optional) tracking database and run the pipelines.
3. Spreadsheet validation - instructions for data submitters who want to validate an import spreadsheet.
4. Information for developers - how to develop the code and run the tests.