ncov-qa

ncov-qa is the workflow used for the quality assessment of COVID-19 data from participating institutes in Ontario. Each institute provides results from FAST5/FASTQ files distributed by Public Health Ontario.

Installation

Download the ncov-qa package from GitHub.

git clone https://github.com/simpsonlab/ncov-qa
cd ncov-qa

It is highly recommended to use conda to install dependencies and tools:

conda env create -f workflow/envs/environment.yaml

Once the dependencies have been installed, activate the conda environment:

conda activate ncov-qa

Usage

The files submitted by each institute include:

• summary_qc.tsv

• consensus.fasta

• lineage_report.csv

These files should reside or be linked in a data directory.

A config.yaml file is required to run the pipeline. The file should use the following as a template:

institute_id: "<institute_prefix>"
submitter: "Submitter"
data_root: "data"
consensus_pattern: "{data_root}/{sample}.fasta"
reference: "/path/to/reference_genome.fasta"
mode: "vcf"
summary_sample_name: "{sample}"

To run the pipeline:

snakemake -s /path/to/ncov-qa/workflow/Snakefile --cores num_cores build_snpeff_db
snakemake -s /path/to/ncov-qa/workflow/Snakefile --cores num_cores all

Output

.
├── config.yaml
├── data
├── lineages
│   ├── <institute>_lineage_report.csv
│   └── <institute>_pangolin_version.txt
├── qa_align
├── qa_results
│   └── <institute>.mutation.metadata.tsv
├── snpEff_genes.txt
└── snpEff_summary.html

Compare results to a baseline

To create a merged count table:

python /path/to/ncov-qa/scripts/merge_qa_results.py --file /path/to/output/qa_results/<institute>.mutation.metadata.tsv --ref_file /path/to/baseline/output/qa_results/<institute>.mutation.metadata.tsv

Credits and Acknowledgements

• The quick_align.py script was obtained from ncov-random-scripts

Authors

• Richard J. de Borja [email protected]

• Jared T. Simpson

License

MIT