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martinghunt edited this page Jan 18, 2018 · 9 revisions

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:

Installation - installation instructions for pipeline users.
Spreadsheet validation - instructions for data submitters who want to validate an import spreadsheet.
Information for developers - how to develop the code and run the tests.