CRyPTIC datasets available through new website

The CRyPTIC project ran from 2016 to 2022 and collected >20,000 clinical samples from patients with tuberculosis. Each sample underwent whole genome sequencing and also was inoculated onto a 96-well plate containing 13 different antibiotics at a range of concentrations. We also collated some existing datasets and the project continued to collect data following the original data freeze in April 2020. We’ve also made extensive improvements to how both the genetics and plate images are processed.

Hence although the original dataset is available through an FTP site hosted at the European Bioinformatics Institute, we now have a larger dataset available which has benefited from several improvements that I won’t go into here. These have been deposited in Zenodo and at the time of writing the current version is v3.4.0 and contains 53,897 samples with both genetic and drug susceptibility testing data. To give these data some context I’ve setup a new CRyPTIC project website to replace the one that unfortunately died last year.