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alignment-repo

Repo maintaining a number of pathogen alignments

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

beast-beagle-docker

bioconda-recipes

Conda recipes for the bioconda channel.

bioinformatics_scripts

chatham

Converts images to triangle representation via a hill climbing algorithm.

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.

denver

NeuroEvolution of Augmenting Typologies (NEAT) Implementation in Java

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.

lone_pine

Sequencing dashboard for San Diego County

maximilian

Mosquito metatranscriptomics monitoring pipeline.

monterey

pacificbeach

pismo

primalseq_pipeline

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

primalseq_simulator

A read simulator for the PrimalSeq protocol.

primuxport

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.