Background

In light of the COVID-19 pandemic, we have implemented an easy way to test your sequence data for SARS-CoV-2 using the One Codex platform. View an example here

Our platform supports analysis of data from capture-based enrichment protocols, amplicon sequencing, and RNA sequencing (RNA-seq) of SARS-CoV-2 samples. Once you upload your samples to our platform, they are automatically classified using our One Codex Database. If we detect SARS-CoV-2 in your sample, we will automatically launch our SARS-CoV-2 analysis pipeline and provide you with a report specifically for this virus.

Understanding your results

The report we provide will give you the following information:

  1. Coverage and depth metrics across the SARS-CoV-2 genome
  2. SNP information, including a graph and table 
  3. A Variant Calling Format (VCF) file with detected variants in the SARS-CoV-2 genome
  4. A consensus assembly sequence

We provide an example report for a SARS-CoV-2 constructed sample (Universal Human Reference RNA with the Twist RNA controls spiked in), to let you explore the outputs from this analysis.

Free analysis and data sharing

In an effort to help the community understand and fight the spread of COVID-19 across the globe, we encourage you to share your results with the community. For our part, we will provide this test is free of charge for any results that you make publicly available. Find out how to make your samples available publicly

Note: If you have PHI or other sensitive data associated with your samples, please contact us and we're happy to help set up sharing of your consensus sequences with any appropriate subset of metadata.

Bioinformatics details

First release (March 17, 2020 – Job ID cc40f34a9a8d4b42 )

The current bioinformatics pipeline consists of a minimal version of Snippy (v4.6.0) but using minimap2 instead of BWA for mapping. Variant calls are made via freebayes and consensus sequences generated via bcftools.

April update (April 1, 2020 – Job ID b45241df22b043a9)

An updated pipeline using ivar for variant calling and consensus sequence generation. This release also includes: (1) support for ARTIC (v1) amplicon sequencing; (2) additional data in the PDF report; and (3) more obvious links to download the BAM files, consensus sequences, and variants TSV. Code is open source and available on GitHub: https://github.com/onecodex/sars-cov-2


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