Description

Bootstrap sample demixing by resampling each site based on a multinomial distribution of read depth across all sites, where the event probabilities were determined by the fraction of the total sample reads found at each site, followed by a secondary resampling at each site according to a multinomial distribution (that is, binomial when there was only one SNV at a site), where event probabilities were determined by the frequencies of each base at the site, and the number of trials is given by the sequencing depth.

Input

Name
Description
Pattern

0 ()

1 ()

2 ()

repeats (integer)

Number of bootstrap repeats to perform

barcodes (file)

File containing lineage defining barcodes

*barcodes.csv

lineages_meta (file)

File containing lineage metadata that correspond to barcodes

*lineages.json

Output

Name
Description
Pattern

0 ()

0 ()

0 ()

Tools

freyja Documentation

Freyja recovers relative lineage abundances from mixed SARS-CoV-2 samples and provides functionality to analyze lineage dynamics.

https://github.com/andersen-lab/Freyjadoi: 10.1038/s41586-022-05049-6License: BSD-2-Clause
Authors