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).
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.
Method for manipulating the "demixed" output files.
This resulting aggregated data can analyzed directly as a tsv file, or can be visualized using freyja plot and freyja dash.
Method provides a fractional abundance estimate for all aggregated samples.
A time(s) metadata CSV file should have Sample,sample_collection_datetime form:
sample_0.tsv,03/01/21
sample_1.tsv,03/03/21
sample_2.tsv,03/08/21
sample_3.tsv,03/10/21
or Sample,sample_collection_datetime,viral_load form:
sample_0.tsv,03/01/21,460326
sample_1.tsv,03/03/21,176645.1
sample_2.tsv,03/08/21,449891.7
sample_3.tsv,03/10/21,361699.5
Note: sample_collection_datetime can have either MM/DD/YY or YYYY-MM-DD format.
Functionality to rapidly prepare a dashboard web page, directly from aggregated freyja output.
A sample(s) metadata CSV file should have this form:
Sample,sample_collection_datetime,viral_load
sample_0.tsv,03/01/21,460326
sample_1.tsv,03/03/21,176645.1
sample_2.tsv,03/08/21,449891.7
sample_3.tsv,03/10/21,361699.5
Note: sample_collection_datetime can have either MM/DD/YY or YYYY-MM-DD format.