Nextclade

Nextclade performs alignment, mutation calling, clade assignment, quality control, and phylogenetic placement of viral genomes to support molecular surveillance of pathogens such as SARS-CoV-2.

Key Features:

• Genome Alignment: Aligns viral genomes to a reference sequence for comparative analysis.
• Mutation Calling: Calls genetic variations and mutations relative to the reference sequence.
• Clade Assignment: Assigns sequences to clades or variants to classify virus strains, including SARS-CoV-2 lineages.
• Quality Control Metrics: Computes multiple quality-control metrics to assess reliability of whole-genome sequencing data.
• Phylogenetic Placement: Places sequences in a phylogenetic context to infer evolutionary relationships among viral genomes.

Scientific Applications:

• Molecular Surveillance: Supports monitoring of variants of concern (VoCs) and other pathogen variants for SARS-CoV-2 and related viral surveillance efforts.
• Genomic Epidemiology: Enables classification and tracking of viral strains using whole-genome sequencing data.
• Sequence Quality Assessment: Provides QC metrics to evaluate sequencing data quality prior to downstream analyses.
• Phylogenetic Analysis: Facilitates placement and interpretation of viral genomes in evolutionary and phylogenetic studies.

Methodology:

Performs reference-based alignment, mutation calling relative to the reference, clade assignment, calculation of quality-control metrics, and phylogenetic placement.