CosmosID-HUB COVID-19
CosmosID-HUB COVID-19
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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