Running ncov tools

ncov-tools uses snakemake to run and execute the QC workflow. The workflow consists of 4 stages: Coverage plots Phylogenetic analysis of SNPs across all samples Generate reports Create a summary report for a given run (optional)

Coverage plots

To generate the coverage plots, the following command can be executed:

snakemake -s workflows/Snakefile —cores <number of cores> all_qc_sequencing

This will generate the following plots (described in Results>Plots):

• _depth_by_position.pdf
• _depth_by_position_negative_control.pdf
• _amplicon_depth_by_ct.pdf
• _amplicon_covered_fraction.pdf
• _genome_completeness_by_ct.pdf

Phylogenetic SNP tree

To create the SNP phylogenetic tree with corresponding heatmap, the following command can be run:

snakemake -s workflows/Snakefile —cores <number of cores> all_qc_analysis

This will also create a text file containing detected SNPs from the consensus genomes in the run named qc_analysis/alleles.tsv.

Generate reports

To generate the control reports and the summary QC table, run:

snakemake -s workflows/Snakefile —cores <number of cores> all_qc_reports

This step will generate the following reports (further described in Results>Reports):

• _summary_qc.tsv
• _ambiguous_position_report.tsv
• _mixture_report.tsv
• _negative_control_report.tsv

Run all workflows

A general workflow rule was created to execute all_qc_sequencing, all_qc_analysis, all_qc_reports:

snakemake -s workflows/Snakefile —cores <number of cores> all

Once the rule is complete, all the output listed above will be generated.