TB-Profiler

Welcome to the documentation for TB-Profiler

TB-Profiler is a command-line tool used to process whole genome sequencing data to predict lineage and drug-resistance. 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 bcftools (or GATKv4/freebayes) to call variants.

Here is an example schematic for illumina paried-end data

Head on over to the next pages to install and learn more about the pipeline.