The CosmosHUB-COVID-19 module is a web based app that supports automated bioinformatics analysis engine for ARTIC V3 protocol, Swift Normalase™ Amplicon SARS-CoV-2 Panel (SNAP) kit, NEXTFLEX® Variant-Seq™ SARS-CoV-2 Kit and Thermofisher Ion AmpliSeq SARS-CoV-2 Insight Research Assay. The bioinformatics analysis results are summarized in an automated PDF report highlighting the Pangolin variant Lineage, NextClade variant clade assignment for CDC’S SARS-CoV-2 variant of interest (VOIs) and variant of concern (VOCs) tracking and surveillance. Additionally, the SARS-CoV-2 consensus created using the app can be easily submitted to public repositories like NCBI and GISAID for national and international SARS-CoV-2 variants surveillance.


CosmosID-HUB COVID-19User Friendly and Intuitive UI

  • Drag and drop Illumina paired-end and single-end raw reads or open file browser to upload data
  • Samples analyzed automatically once uploaded to the platform

CosmosID-HUB COVID-19Comprehensive analysis and reporting

  • Download PDF reports and an aggregated summary
  • For each sample, ability to export:
    • Consensus SARS-CoV-2 fasta
    • Variant calling stats tsv
    • BAM file
    • Mapping stats summary file

CosmosID-HUB COVID-19Automated PDF Report highlighting the important findings for each sample

  • Summary
    • How many reads were generated for a given sample 
    • How many reads (total and in %) were mapped to the SARS-CoV-2 reference genome 
    • How evenly, and how deeply the NGS reads cover the SARS-CoV-2 genome
    • The Pangolin lineage and the NextClade Clade of the sequenced SARS-CoV-2 strain. 
  • Coverage Plot
  • The Pangolin Lineage Assignment is highlighted Red if the determined lineage falls under the CDC’s list of variants of concern or variants of interest

CosmosID-HUB COVID-19Aggregated summary CSV makes it easier to discern interesting pattern from a large sequencing run

  • Comprehensive summary of every sample in one file
  • An entire sequencing run’s QC and important findings summarized in a table within minutes
  • Aggregated summary makes it simpler and flexible for researchers and clinicians to screen, discern and convey important SARS-CoV-2 genomic surveillance patterns to the public health personnel

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