SARS-CoV-2 workflows

The SARS-CoV-2 workflows

Two workflows are available for analyzing SARS-CoV-2 data (figure 4.1), one workflow is customized for use with Ion AmpliSeq SARS-CoV-2 Research Panel data and the other is customized for use with QIAseq SARS-CoV-2 Panel data. Both 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 4.1: The available SARS-CoV-2 ready-to-use 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 potential variants, those with frequencies between 20% and 50%. Potential 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 Large MLST Scheme Tools in for further details.