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TBProfiler Container

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.

Database

This tool relies on a database to run. The version (AKA git commit hash) of the database that is included in the docker image is 97b5876. This is from the GitHub repository https://github.com/jodyphelan/tbdb. This can be confirmed in the json file: /opt/conda/share/tbprofiler/tbdb.version.json:

$ grep 'commit' /opt/conda/share/tbprofiler/tbdb.version.json
{"name": "tbdb", "commit": "5f3c51e", "Merge": "b1a2549 abddb8e", "Author": "Jody Phelan <[email protected]>", "Date": "Thu Jan 19 10:47:32 2023 +0000"}

Additionally you can run the command tb-profiler list_db to list the same information

$ tb-profiler list_db
tbdb    97b5876 Jody Phelan <[email protected]>   Wed May 8 13:53:15 2024 +0100   /opt/conda/share/tbprofiler/tbdb

Additional included tools/dependencies

  • bedtools 2.31.1
  • gatk4 4.5.0.0
  • kmc 3.2.4
  • pathogen-profiler 4.2.0
  • perl 5.32.1
  • python 3.10.14
  • trimmomatic 0.39
  • bwa 0.7.18
  • minimap2 2.28
  • samtools 1.20
  • bcftools 1.20
  • freebayes 1.3.6
  • tqdm 4.66.4
  • parallel 20240522
  • samclip 0.4.0
  • snpeff 5.2

Example Usage

Run whole pipeline on Illumina paired-end reads:

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>

Updates

Release 5.0.1 implemented sqlite3 database locking with https://py-filelock.readthedocs.io/en/latest/index.html. This should fix issues using it over network filing systems (NFS). For more information, official documentation can be found here.