# 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](/files/-M9d_diTzl9Ae2kLM03R) Head on over to the next pages to install and learn more about the pipeline. --- # Agent Instructions: Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter: ``` GET https://jodyphelan.gitbook.io/tb-profiler/master.md?ask= ``` The question should be specific, self-contained, and written in natural language. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.