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beast-flow

Nextflow pipeline for estimation of evolutionary rate using Bayesian statistics.

covflo

Nextflow pipeline for generation of BCCDC routine SARS-CoV-2 phylogenetic trees to be visualized with Auspice.

divirusity

Quantify viral genetic diversity within hosts from NGS data (paired-end raw reads) without needing to reconstruct full-length haplotypes.

fluflo

Nextflow pipeline for generation of phylogenetic trees to be visualized in Auspice.

phip-flow

A Nextflow pipeline to align, merge, and organize large PhIP-Seq datasets

snperr

Determine read depth and variant frequency thresholds to distinguish NGS sequencing errors from true SNPs. Simulates effect of changing per-site read depth and variant frequency on accuracy of genetic diversity measures (pi, alterante allele frequency, shannon diversity).

snpgenie

Program for estimating πN/πS, dN/dS, and other diversity measures from next-generation sequencing data

swampy