SARS-CoV-2 WGS Analysis Report

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1 GMS-Artic pipeline

The GMS-Artic aims to develop a nationwide standard open-source bioinformatic workflow to investigate SARS-CoV-2 whole genome sequencing for real-time clinical practices on the National Genomic Platform (NGP). A parallel work using the GMS-Artic framework designed to update all metadata information from the clinics and upload the output result to the Swedish Health Agency routinely. Continuous support on the pipeline development and an additional process like variant visualization is currently in progress.
The following analysis result is generated using the GMS-Artic v2.0.0. For details, please visit GitHub repo.

1.1 Quality Checks

1.1.1 QC parameters settings

1.1.2 QC results from Pangolin

*Description

1.2 Alignment Statistics

1.3 Lineage analysis

1.3.1 NextClade and Pangolin Table

1.3.2 Scorpio Table

1.4 VCF

1.5 Depth plot

1.6 Tools used and versions

Link to NextFlow Run - Please NOTE: This will works local only - where the pipeline runs

1.6.1 Container tools: versions

Details are provided below:

1.6.2 NextFlow timeline

Open in a new tab - Please NOTE: This will works local only - where the pipeline runs