idCOV

idCOV identifies SARS-CoV-2 clades from raw FastQ sequencing reads using a predefined set of clade-defining genetic markers for phylogenetic classification.

Key Features:

• Clade Identification: Uses a curated list of clade-defining genetic markers to classify SARS-CoV-2 isolates and align calls with established systems such as Nextstrain.org.
• Raw Read Processing: Accepts raw FastQ sequencing files and processes sequencing reads for clade determination.
• Validation: Empirical validation on a public dataset shows clade calls consistent with Nextstrain.org annotations across three common clade classification systems.

Scientific Applications:

• Epidemiological Surveillance: Provides clade assignments to support outbreak tracking and public health surveillance of SARS-CoV-2.
• Viral Evolution Tracking: Enables monitoring of lineage evolution and mutation patterns in SARS-CoV-2 isolates over time.
• Variant Monitoring and Vaccine Analyses: Facilitates detection of emerging variants and supports analyses relevant to vaccine development and effectiveness studies.

Methodology:

Processes raw FastQ sequencing reads through a computational pipeline that uses a predefined list of clade-defining genetic markers to assign SARS-CoV-2 isolates to clades.