watronfire

Vercingetorix

T cell receptor repertoire analysis.

COVID-19-Testing-Results

Collecting COVID-19 testing data from around the world

CViSB_Workshop_TCells

Tutorial on T cell identification and characterization using single cell RNA-seq data for CViSB's 2020 Workshop.

beast-beagle-docker

Alignment-Repo

Repo maintaining a number of pathogen alignments

augur

Pipeline components for real-time phylodynamic analysis

baltic

baltic - backronymed adaptable lightweight tree import code for molecular phylogeny manipulation, analysis and visualisation. Development is back on the evogytis/baltic branch (i.e. here).

baltic-examples

Examples of using the Baltic plotting library

bioconda-recipes

Conda recipes for the bioconda channel.

Eureka

Snakemake pipeline for analysis of pathogen genomes. Will be pathogen-agnostic in the future but is currently designed for *Vibrio Cholerae*

FAVITES

FAVITES (FrAmework for VIral Transmission and Evolution Simulation)

geosketch

HCoV-19-Genomics

SARS-CoV-2 genomics

Hoonah

iVar

Confirms intrahost variants with sequencing replicates.

Maximilian

Mosquito metatranscriptomics monitoring pipeline.

monterey

Pismo

PrimalSeq_Pipeline

Snakemake pipeline for processing sequencing reads generated with the PrimalSeq v4 protocol.

PrimalSeq_Simulator

A read simulator for the PrimalSeq protocol.

project_2023_WNV_transmission

Public-CV

LaTeX template for my CV

public_health_bioinformatics

Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of pathogens of public health concern.

sarscov2-adaptive-evolution

snakemake-broad-uger

Snakemake profile to execute workflows on the Broad Institute UGER cluster

Taos

De novo development of poker strategy.

Tialoc

ubba

Tools for processing of single cell data and benchmarking of batch correction techniques

WARN-ID_training

Scripts to setup laptops for ACEGID training.

watronfire.github.io