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atom-language-nextflow

Nextflow syntax highlighter for Atom editor

betabinomial_bottleneck

Code for estimating transmission bottleneck sizes using the betabinomial approach

cva10_guangdong

This repository including the code for phylogenetic analysis in paper 'Genomic Epidemiology of CVA10 in Guangdong, China 2013-2021'

delta-variant-outbreak-in-gz

The pipeline for calling variants and generated consensus sequences from NGS data generated in this study

fieldbioinformatics

The ARTIC field bioinformatics pipeline

jcvi

Python library to facilitate genome assembly, annotation, and comparative genomics

medaka

Sequence correction provided by ONT Research

ncov

Nextstrain build for novel coronavirus SARS-CoV-2

ncov-narrative

ncov_cohort

This repository including the pipeline for phylogenetic analysis and the code for making figures in the submitted paper

seirsplus

Models of SEIRS epidemic dynamics with extensions, including network-structured populations, testing, contact tracing, and social distancing.

sewage-norovirus-surveillance

This pipeline and R scrips are used to analyze the norovirus genotypes distribution in sewage through amplicon NGS

variant_pipeline

Work on the variant_pipeline and initial r analysis used in calling variants from NGS data

wf-artic

ARTIC SARS-CoV-2 workflow and reporting