EDGE COVID-19

EDGE COVID-19 performs integrated analysis of SARS-CoV-2 sequencing data to generate submission-ready consensus genomes, assign lineages, and support genomic surveillance.

Key Features:

• Integrated Bioinformatic Workflows: Workflows tailored for SARS-CoV-2 data generated using Illumina and Oxford Nanopore Technologies (ONT).
• Automated Data Quality Control: Automated initial data quality control steps to filter and process raw sequencing data.
• Consensus Genome Generation: Reference-based genome variant calling to produce consensus genomes for SARS-CoV-2.
• Lineage Determination: Lineage assignment of SARS-CoV-2 strains to characterize genetic diversity and evolutionary dynamics.
• Data Submission Capabilities: Generation of consensus sequences and metadata formatted for submission to GenBank, GISAID, and INSDC raw data repositories.
• Validation on Real-World and Test Datasets: Accuracy of variant and lineage analyses validated against multiple test and real-world datasets.
• Comparative Analysis with Existing Workflows: Direct comparisons of EDGE COVID-19 workflows with the COVID-19 Galaxy Project workflows.
• Sequencing Technology Insights: Analyses comparing outcomes and patterns observed when using Illumina versus ONT technologies.

Scientific Applications:

• Genomic Surveillance: Produces submission-ready consensus genomes to support population-level monitoring of SARS-CoV-2.
• Epidemiological Investigation: Provides lineage assignments and variant calls to inform transmission and outbreak analyses.
• Variant Tracking and Evolutionary Analysis: Enables detection and characterization of mutations to study viral evolution and diversity.

Methodology:

Automated data quality control, reference-based genome variant calling to generate consensus genomes, lineage determination, comparative analyses with the COVID-19 Galaxy Project workflows, and validation against test and real-world datasets.