COVID‑DX: commercial grade software built by researchers for researchers

Why choose COVID‑DX

Our COVID-DX software is built for researchers identifying and characterizing the genetic profile of SARS-CoV-2 samples. Researchers upload sequence data through our user portal and download a comprehensive and accessible report, which profiles genetic variants, lineages, phylogenetic analysis, and coverage. Our report also provides additional insights and annotations of key variants according to the CDC.

COVID-DX has been optimized and extensively validated for amplicon-based (ARTIC), and hybridization-capture (Twist) based SARS-CoV-2 sequencing approaches, but may also work for other sequencing approaches.

Critical insights

Comprehensive Variant Profiling

Lineages
Coverage
Clade, phylogenetic analysis

Static Pipeline, Dynamic Database

Up-to-date variant curation in accordance with CC recommendations

Ease of use

User Friendly Portal, Powerful Reporting

Order Tests
Upload FAST files for analysis
Download test report
GISAID submission ready files

*No bioinformatics expertise needed

Scientific rigor

Commercial-Grade Software

An FDA vetted bioinformatics platform
Developed in our CLIA certified lab
Pre-processing & quality control included

Versatility

One-Stop-Shop Covid Analytics

Compatible with amplicon-based & hybrid capture platforms
Individual or batch upload options
Customizable output (PDF, research output, GISAID submission support)

Report features

Data analysis and reporting

The Biotia COVID-DX software analyzes sequencing results to provide a clinically oriented report that includes results on the presence or absence of the SARS-CoV-2 virus in each sample.

We also provide a research-use only version of the software, which is optimized for other lab kits, and which generates a report including comprehensive profiling of variants as described in more detail below.

Presence/absence

Detection of SARS-CoV-2 is based on the percentage of the viral genome that is recovered from a patient's sample. The higher the percentage of viral genome that is recovered, the more likely it is that the assay will determine that the virus is present.

Coverage plot

Detection of the SARS-CoV-2 virus is based on the amount of the genome recovered from sequencing a sample. The plot shows the depth of sequencing that was recovered across the genome. Coverage refers to the percent of the SARS-CoV-2 genome that was covered by at least one read from sequencing. Coloring is based on confidence in calling a variant at a given location (output from GATK Callable Loci) with no coverage (pink), low coverage (grey), and higher callable coverage (blue) shown.

The diagram also demonstrates the positions of the genes within the SARS-CoV-2 genome so that users can see which regions of the genome, if any, have low or missing coverage.

Genetic variants

Genetic variants, lineages, and clades are determined by aligning the test strain to the SARS-CoV-2 reference genome (NC_045512.2) with information on gene location/site, and alteration provided. Key variants identified by the CDC are also annotated in the report to provide further insight.

Phylogenetic analysis

We place your sample in a phylogenetic tree of SARS-CoV-2 samples built from geographically labeled samples in GISAID and our own database of variants. Samples are labeled by their similarity to different known clades and geographic identities.