To download all the pipelines:
git clone https://github.com/iframst/HybridAMRg.git
cd HybridAMRg/pipelines
Run a pipeline
bash <pipeline_name>.sh
## example
bash Genomic_hybrid.sh
Inputs
Each pipeline takes as input a file or directory containing fastq reads. The pipeline is designed to take a single sample as input, multiple samples can be run by looping the bash script.
Outputs
A directory containing results of each sub-program, and the final assembly with corresponding annotation report. Outputs are named acording to the input file or directory.