Freyja: Bootstrapping (version 2.0.1+galaxy0)

Variants file:

Sequencing depth file:

Source of UShER barcodes data:

Freyja ships with an usher_barcodes.csv file, which the tool can access internally. Since this file gets updated rather frequently, you can also download the latest version of the file from https://github.com/andersen-lab/Freyja/raw/main/freyja/data/usher_barcodes.csv, set the dataset's datatype to csv and use it as a custom barcodes file.

Custom lineage metadata file:

For additional flexibility and reproducibility of analyses, a custom lineage-to-contellation mapping metadata file can be provided.

Minimum lineage abundance tp include:

e.g. 0.0001.

Remove unconfirmed lineages from the analysis:

If the UShER tree includes proposed lineages, the --confirmedonly flag removes unconfirmed lineages from the analysis.

Use larger library with non-public lineages:

Allows to use larger UShER barcodes library extended with GISAID non-public lineages

Pathogen of interest:

Number of bootstraps:

Generate boxplot:

What it does

Freyja is a tool to recover relative lineage abundances from mixed SARS-CoV-2 samples from a sequencing dataset (BAM aligned to the Hu-1 reference).

General information

Freyja is a tool to recover relative lineage abundances from mixed SARS-CoV-2 samples from a sequencing dataset (BAM aligned to the Hu-1 reference). The method uses lineage-determining mutational "barcodes" derived from the UShER global phylogenetic tree as a basis set to solve the constrained (unit sum, non-negative) de-mixing problem.

Freyja is intended as a post-processing step after primer trimming and variant calling in iVar (Grubaugh and Gangavaparu et al., 2019). From measurements of SNV freqency and sequencing depth at each position in the genome, Freyja returns an estimate of the true lineage abundances in the sample.

Information about freyja boot method

A fast bootstrapping method for freyja.

Outputs

Bootstrapping method results:

Bootstrap lineages: the 0.025, 0.05,0.25,0.5 (median),0.75, 0.95, and 0.975 percentiles for each lineage;
Bootstrap summarized: WHO designated VOI/VOC