Overview

Freyja is a tool used to analyze SARS-CoV-2 wastewater genomic sequencing data. Developed by Josh Levy from the Andersen Lab, it performs two main steps: (1) SNV frequency estimation, and (2) depth-weighted demixing using constrained least absolute deviation regression. Additional post-processing steps can produce visualizations of aggregated samples.

Four workflows have been created that perform different parts of Freyja:

Freyja_FASTQ runs various QC modules before aligning the sample with BWA and using iVar for primer trimming. After the preprocessing is completed, Freyja is run to demix the sample. Optional bootstrapping may be performed.
Freyja_Plot aggregates multiple samples using output from Freyja_FASTQ to generate a plot that shows fractional abundance estimates for all samples, with the option to plot with sample collection date information.
Freyja_Dashboard aggregates multiple samples using output from Freyja_FASTQ to generate an interactive visualization. This workflow requires an additional input field called viral load, which is the number of viral copies per liter.
Freyja_Update will copy the reference files (used in Freyja_FASTQ) found in the Docker image to a user-specific Google Cloud Storage location.

A typical wastewater analysis on Terra will begin with Freyja_FASTQ and will be followed by either Freyja_Plot and/or Freyja_Dashboard. Freyja_Update is run whenever the Freyja Docker image is updated.

Workflows available

Overview

Freyja_FASTQ

Freyja_Plot

Freyja_Dashboard

Freyja_Update

References