New Zealand Tuberculosis Drug Resistance Pipeline
This pipeline was intended to be used within New Zealand for clinical purposes and was part of a 2019 Honours project.
This pipeline will perform variant calling on raw sequences, and identify drug-conferring SNPs. Processed samples will be automatically stored within a repository, as well as produce a clinical report on drug-susceptibility.
The resistance pipeline is designed to be flexible for a range of situations. Primarily, the pipeline has been designed so that clinicians will have a user-friendly experience.
There are two methods for the pipeline to detect resistance mutations
Placing sequences within the input directory
If no sequences are provided, the pipeline will search the input directory for sequences.
resistance.sh
Providing sequencing files
The user can specify forward and reverse reads for processing
resistance.sh --forward /sequences/sample_1_R1.fastq.gz --reverse /sequences/sample_1_R1.fastq.gz
Software needed to run
- Python 3.7.1
- Fastq-mcf v1.04.807
- BWA v0.7.17-r1188
- Samtools v1.9 (htslib 1.9)
- Bcftools v1.9 (htslib 1.9)
- Freebayes v1.3.1-dirty
It is recommended that you perform a dry-run when setting up for the first time:
Dry Run
resistance.sh --setup
After completing the dry-run, the pipeline will exit and be ready for use. The set-up log files can also be consulted for issues with the setup.
Alternatively, the pipeline can detect if the pipeline has not been set-up, and will configure the environment before running.
- Jordan Taylor - Bioinformatician - University of Otago
- Person 1
- Person 2
- Reason 1