Tbprofiler
Description
The tbprofiler pipeline aligns reads to the H37Rv reference using bowtie2, BWA or minimap2 and then calls variants using bcftools. These variants are then compared to a drug-resistance database. We also predict the number of reads supporting drug resistance variants as an insight into hetero-resistance (not applicable for minION data)
Environment Modules
Run module spider tbprofiler to find out what environment modules are available for this application.
System Variables
- HPC_TBPROFILER_DIR - installation directory
Citation
If you publish research that uses tbprofiler you have to cite it as follows:
Phelan, J., O’Sullivan, D.M., Machado, D. et al. Integrating informatics tools and portable sequencing technology for rapid detection of resistance to anti-tuberculous drugs. Genome Med 11, 41 (2019). https://doi.org/10.1186/s13073-019-0650-x