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README.md

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 2c92475. This is from the GitHub repository https://github.com/jodyphelan/tbdb. This can be confirmed in the json file: /opt/conda/share/tbprofiler/tbdb.variables.json:

$ grep 'commit' /opt/conda/share/tbprofiler/tbdb.variables.json
{"db-schema-version": "1.0.0", "snpEff_db": "Mycobacterium_tuberculosis_h37rv", "drugs": ["rifampicin", "isoniazid", "ethambutol", "pyrazinamide", "moxifloxacin", "levofloxacin", "bedaquiline", "delamanid", "pretomanid", "linezolid", "streptomycin", "amikacin", "kanamycin", "capreomycin", "clofazimine", "ethionamide", "para-aminosalicylic_acid", "cycloserine"], "tb-profiler-version": ">=6.0.0,<7.0.0", "version": {"name": "tbdb", "commit": "2c92475", "Merge": "8918884 2a51937", "Author": "Jody Phelan <[email protected]>", "Date": "Mon Oct 7 17:06:42 2024 +0100", "db-schema-version": "1.0.0"}, "amplicon": false, "files": {"ref": "tbdb.fasta", "gff": "tbdb.gff", "bed": "tbdb.bed", "json_db": "tbdb.dr.json", "variables": "tbdb.variables.json", "spoligotype_spacers": "tbdb.spoligotype_spacers.txt", "spoligotype_annotations": "tbdb.spoligotype_list.csv", "bedmask": "tbdb.mask.bed", "barcode": "tbdb.barcode.bed", "rules": "tbdb.rules.txt"}}

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

$ tb-profiler list_db
tbdb    2c92475 Jody Phelan <[email protected]>   Mon Oct 7 17:06:42 2024 +0100   /opt/conda/share/tbprofiler/tbdb

Additional included tools/dependencies

  • bedtools 2.31.1
  • gatk4 4.6.1.0
  • kmc 3.2.4
  • pathogen-profiler 4.5.0
  • perl 5.32.1
  • python 3.12.3
  • trimmomatic 0.39
  • bwa 0.7.18
  • minimap2 2.28
  • samtools 1.21
  • bcftools 1.21
  • freebayes 1.3.6
  • tqdm 4.66.6
  • parallel 20240922
  • samclip 0.4.0
  • snpeff 5.2
  • delly 1.2.6 (the more recent version 1.3.1 did not allow for the conda environment to resolve. More info here: jodyphelan/TBProfiler#393 (comment))

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.