The BTK handbook

We have created a BTK handbook to help you install the pipeline and run it locally on your own assembly. It can be downloaded as a PDF here.

This handbook is a work in progress. To access the latest live version at any time, you can go to the GitHub page.

We know all the steps work on our servers and systems, but the installation has not been comprehensively tested. We are actively revising the steps in response to any comments specific to other computers, so we recommend that you also check out the live version on GitHub as your issue might already have been fixed there. Please do report any snags you might find so that we can improve the materials.

Using test data

The BTK pipeline involves many steps and many different tools. Therefore it is a good idea to run the entire pipeline with the example test data and test databases provided in the handbook first to see that it is installed correctly. Running BTK on all the public data at once is likely to be very slow, so not useful for testing. Once you have got everything working correctly with the test data, you can download the full databases and run the full pipeline on your full assembly.

How to get help

If you have any trouble running installing BTK, or running any of the steps in the BTK handbook, please check the GitHub issues board as someone else may have had the same problem before.

Please use the GitHub issues link above rather than the comments section below this article if you have any questions. We will only be monitoring the comments here for a couple of weeks after the course ends. We will be monitoring the issues board and will be happy to respond there so that the answers are useful to the wider community of BTK users rather than just the attendees of this course.