Welcome to the webserver of NTM-Profiler - a pipeline which allows users
to analyse Mycobacterial 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.
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
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 markers have been retreived from the literature.
You can take a look at the
up to date CSV files
here by navigating to the
relevant species folder and viewing the
variants.csv file.
Can I run NTM-Profiler on my own computer?
If you have access to a linux or macOS operating system then you can download
the commandline version of NTM-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 NTM-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
Please cite this website if you use it in your research.
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.
