j3551ca

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.

epyflu

Consolidated upload, download, and record-keeping of Influenza isolates with GISAID EpiFlu.

fluflo

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

gisflu

Access the GISAID Flu database using Python

kma-cgmlst

A cgMLST pipeline based on the KMA aligner

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

WasteFlow

Nextflow pipeline for pathogen surveillance in wastewater