This is the updated pipeline for APHA's processing of Mycobacterium bovis WGS data. BovTB-nf is designed to process a batch (1 or more samples) of paired-end fastq files generated on an Illumina sequencer. It will first remove duplicate reads from the dataset (FastUniq) and then trim the unique reads based on base-call quality and the presence of adapters (Trimmomatic). Reads are then mapped to the M. bovis AF2122 reference genome and variants called (bwa/samtools/bcftools).
It has been built to run using nextflow, using standard bioinformatic tools for the most part. The external dependancies are:
- FastUniq
- Trimmomatic
- bwa
- samtools and bcftools
- vcfutils.pl
- Kraken2 (and database)
Of course Nextflow itself is a prerequisite and should be installed as described in the Nextflow Documentation
If you have the dependancies installed the pipeline can run by simply typing:
nextflow run ellisrichardj/BovTB-nf
Alternatively, clone the repository:
git clone https://github.com/ellisrichardj/BovTB-nf.git
If required, there is simple script for installing the dependancies (helpfully called Install_dependancies.sh), which will also update the nextflow config file with their locations.
In its simplest form just run the Nextflow process from the directory containing the fastq files:
cd /path/to/Data
nextflow run BovTB-nf