README.md

covid_assembly_pipeline

This is a wrapper pipeline for the https://github.com/mjsull/COVID_pipe repo. This wrapper pushes the data to PathogenDB.

To run this pipeline first clone this repo and create the conda environment for it to run in.

cd <this directory>

conda env create --file env.yml

Test if the conda environment works: conda activate covid

you may need to update conda before creation

conda update conda

Edit covid_assembly_pipeline_wrapper_example.sh script and run the pipeline using the following command

./covid_assembly_pipeline_wrapper.sh <run_folder>/<sample_folder>

The pipeline automatically determines Thermo vs Illumina libraries and runs accordingly.

The run folder name must be in the following format

<runID_pipeline>

The following folder structure should exist for <sample_folder>

<sample_folder>
└───<sample_library1>'
│   │   <read_prefix>_R1_001.fastq.gz
│   │   <read_prefix>_R2_001.fastq.gz
│
└───<sample_library2>
    │   <read_prefix>_R1_001.fastq.gz
    │   <read_prefix>_R2_001.fastq.gz

n.b. can be run on one to as many read files as needed, each pair of reads should have it's own folder.

The pipeline creates all the output data in <sample_folder> and pushes the assembly info to pathogenDB.