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bactmap

A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences

biobash

A collection of bash scripts for bioinformatics

dryad

Dryad is a pipeline to construct reference free core-genome or SNP phylogenetic trees for examining prokaryote relatedness in outbreaks.

github-slideshow

A robot powered training repository :robot:

harvest-tools

introducing-python

An introduction to Python

introtodatascience

GitHub Repository to accompany my YouTube series of videos on Introductory Data Science using R.

lockdown_learning

mumps

Nextstrain build for mumps virus

mumps-seq

Protocols for sequencing mumps viruses

oneliners

Useful bash one-liners for bioinformatics.

public_health_viral_genomics

pythonforbioinformatics

This repository will be helpful to start using python for your Bioinformatics projects.

rscripts

sars-cov-2_sequencing

A collection of sequencing protocols and bioinformatic resources for SARS-CoV-2 sequencing.

sarscov2recombinants

Scan SARS-SoV-2 sequences for potential recombinants

seqtk

Toolkit for processing sequences in FASTA/Q formats

staphb_toolkit

Python Toolkit for using containerized programs in either Singularity or Docker

tb_molecular_epidemiology

Algorithms for TB molecular epidemiology analysis

tormes

Making whole bacterial genome sequencing data analysis easy

viral-pipelines

viral-ngs: complete pipelines

wdl

Workflow Description Language - Specification and Implementations