Main tool: TBProfiler
The 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. It also predicts the number of reads supporting drug resistance variants as an insight into hetero-resistance.
This tool relies on a database to run. The database that is included in the docker image is 4738132. This is from the Git repository https://github.com/jodyphelan/tbdb. This can be confirmed in the json file:./TBProfiler-${TBPROFILER_VER}/db/tbdb.version.json:
{"name": "tbdb", "commit": "c2fb9a2", "Author": "jodyphelan <jody.phelan@lshtm.ac.uk>", "Date": "Tue Oct 4 11:40:15 2022 +0100"}
Run whole pipeline:
tb-profiler profile -1 ERR1664619_1.fastq.gz -2 ERR1664619_2.fastq.gz -t 4 -p ERR1664619 --txt
Make alternative database:
tb-profiler create_db --prefix <new_library_name>
tb-profiler load_library --prefix <new_library_name>
Better documentation can be found here.