SARS-CoV-2 workflows

The SARS-CoV-2 workflows

Three workflows are available for analyzing SARS-CoV-2 data (figure 16.1), one workflow is a generic workflow for use with ARTIC V3 SARS-CoV-2 primers designs, one workflow is customized for use with Ion AmpliSeq SARS-CoV-2 Research Panel data and the last workflow is customized for use with QIAseq DIRECT SARS-CoV-2 Panel data. All workflows can take one or multiple samples as input, which allows for analysis of a single sample or comparison of multiple samples based on a single workflow run.

The general approach of both workflows is mapping the reads to a reference, generating a consensus sequence from the mapping, calling variants, and generating outputs that allow for efficient review of results, including cross-sample comparison.

Image sarscov2wffolder
Figure 16.1: The available SARS-CoV-2 template workflows

Two variant tracks are produced by each workflow, one containing variants likely to be true variants, those with frequencies between 50% and 100%, and another containing all potential variants, called low frequency variants with defaults down to between 10% and 20% depending on sequencing technology. Potential low frequency variants are likely to need further validation, as they may represent new mutations in the sample, but may be due to other factors, for example reverse transcriptase or sequencing errors.

In more detail, each workflow takes this general approach:

Part of each workflow runs on each sample individually, with the per-sample results then being combined to aid inter-sample comparison. Thus, it is assumed that data for multiple samples will be provided when the workflow is launched. If data for only one sample is provided, the workflow will still run, and the results for the individual sample are still valid.

The workflow outputs can be used with the tools in CLC Microbial Genomics Module. Examples include:

Please see the sections on Taxonomic Analysis, Functional Analysis, Phylogenetic trees using SNPs and k-mers and MLST Scheme Tools in for further details.