for SARS-CoV-2 variant identification starting from NGS data
QUALITY CONTROL ASSESSMENT
Quality information about the sequencing data and the genome assembly.
The Nextstrain clade and Pango lineage of the variant sequenced is reported. A VOC (Variant Of Concern) tag is displayed if the variant identification result corresponds to a VOC as specified by the VOC definitions included in the EPISEQ® SARS-COV-2 pipeline. Nextstrain, Pango lineage information and VOC definitions are updated on a weekly basis, clearly versioned in the application.
A list of mutations (amino acid changes) detected in the spike gene (see screenshot) and other genes of the variant sequenced, is reported.
DETAILED SAMPLE REPORT
A sample pdf report is available containing detailed EPISEQ® SARS-COV-2 pipeline results and can be downloaded by the user.
A consensus sequence is created from the reads after alignment against the SARS-CoV-2 reference genome and can be downloaded in FASTA format.
GENOME ALIGNMENT MAPPING
An alignment mapping of the reads against the SARS-CoV-2 reference genome can be downloaded in BAM format.