Viral Consensus Genome Pipeline

The CZ ID viral consensus genomes pipeline was adapted from the initial SARS-CoV-2 genome pipeline released in August 2020 to assemble genomes for viruses listed in the mNGS Sample Report. Now you can upload data to CZ ID for viral genome assembly, which enables you to process samples in bulk. When uploading data directly into the viral consensus genome pipeline, you provide the reference sequence and have the option to include a primer BED file. Therefore, you can upload data obtained through enrichment (e.g., MSSPE), PCR-based, whole genome, or metagenomic sequencing methods to the pipeline. This contrasts with the consensus genome pipeline initiated from the mNGS Sample Report, which is designed to assemble viral genomes from metagenomic samples.

The diagram below summarizes analysis tools implemented through the viral consensus genome pipeline, information included in reports for assembled genomes, and data download options.

The viral consensus genome pipeline was first implemented through the mNGS Illumina Sample Report (see Assembling Genomes from Sample Report). At that time, the pipeline was validated to ensure the assembly of quality consensus genomes. Click here for details about the validation process.