TB-Profiler

Welcome to the webserver of TB-Profiler - a pipeline which allows users to analyse M. tuberculosis whole genome sequencing data to predict lineage and drug resistance. Follow the instructions below to upload a new sample or view analysed runs.
How does it work?
The pipeline searches for small variants and big deletions associated with drug resistance. It will also report the lineage. By default it uses Trimmomatic to trim the reads, BWA (or minimap2 for nanopore) to align to the reference genome and GATK (open source v4) to call variants.
Step 1
Profile your sample

Upload your next generation sequencing data in fastQ format. You can upload one or two (forward and reverse) fastq files. When you upload your data, the run will be be assigned a unique ID. Please take a note of this ID as you will need to to find your results later. Batch upload of samples is also possible.

Upload
Step 2
View the results

Find your results by entering you unique run ID directly into the search box below.

Which mutations are being used to prodict resistance?
Resistance is predicted using the curated tbdb database. This database has been tested using over 17,000 samples with genotypic and phenotypic data. You can read more about the markers present in the library at the time of testing here or you can take a look at the up to date CSV file here.
Need to analyse isolates from the SRA?
To benchmark the performance we have run TB-Profiler for over 16,000 publically available M. tuberculosis isolates. We have made these available here. With each new release of TB-Profiler we will update all result files.
Can I run TB-Profiler on my own computer?
If you have access to a linux or osX operating system then you can download the commandline version of TB-Profiler. For more information on this please visit the github repository. If you would like to create your own instance of this webserver, the code is fully open-source and available at this github repository
Give feedback or request a feature
We are always looking to improve TB-Profiler. If you see some results that don't look right or would like to see some additional functionality in the future, don't hesitate to get in touch via the section on our github page.
Citation
Phelan, J. E. et al. Integrating informatics tools and portable sequencing technology for rapid detection of resistance to anti-tuberculous drugs. Genome Med. 11, 41 (2019).
Coll F, et al. Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences. Genome Medicine 7: 51 (2015).

Disclaimer
This tool is for Research Use Only. It has not been approved, cleared, or licensed by any regulatory authority. By submitting sequence data the user acknowledges no intended medical purpose or objective such as clinical diagnosis, patient management, or human clinical trials.