CoVpipe2

CoVpipe2 reconstructs SARS-CoV-2 genomes from short-read sequencing data with features for primer clipping, mixed sample detection, and recombinant identification to support genomic surveillance.

Key Features:

• Quality Control: Performs fundamental quality control on short-read sequencing data.
• Mapping and Variant Calling: Executes read mapping and variant calling for SARS-CoV-2 genome reconstruction.
• Consensus Generation: Generates consensus sequences from processed sequencing data.
• Primer Clipping: Addresses primer clipping challenges, including mutations near primer sites.
• Mixed Sample Detection: Implements features to detect mixed samples and heterozygote variants.
• Recombinant Detection: Includes capabilities to identify recombinant sequences.
• Low-Coverage and Deletion Handling: Manages low-coverage regions and deletions in genome reconstruction.
• Amplicon and Whole-Genome Compatibility: Specifically addresses short-read amplicon protocols while also supporting whole-genome short-read sequencing data.
• Modular Design: Provides a modular workflow architecture adaptable to different sequencing protocols.

Scientific Applications:

• Genomic Surveillance: Supports tracing of transmission chains, discovery of new viral lineages and mutations, and assessment of infectiousness and treatment resistance.
• Variant Detection: Enables reference-based reconstruction and variant detection for SARS-CoV-2 genomes from amplicon sequencing data.
• Benchmark Validation: Validated against selected publicly available benchmark datasets for accurate genome reconstruction.

Methodology:

CoVpipe2 is written in Nextflow. The workflow performs quality control, mapping, variant calling, and consensus generation, with additional features for detecting mixed samples and recombinants. The pipeline addresses primer clipping, heterozygote variant detection, low-coverage regions, and deletions.