An extensive workflow to process Nanopore and Illumina sequencing for bacterial genomes.

Set up in minutes

Install bactopia from Bioconda and start processing genomes in minutes

Installation

Effortless bacterial genomics

Streamlined pipeline for efficient and complete analysis of bacterial genomes

Beginner's Guide

Seamlessly expand analyses

Rapidly extend studies with a variety of supplementary, ready-made, workflows

Bactopia Tools

Making an impact

A free and open-source tool that regularly contributes back to the community

Impact and Outreach

Overview

Bactopia is a flexible pipeline for complete analysis of bacterial genomes. The goal of Bactopia is process your data with a broad set of tools, so that you can get to the fun part of analyses quicker!

Bactopia was inspired by Staphopia, a workflow targeted towards Staphylococcus aureus genomes. Using what we learned from Staphopia and user feedback, Bactopia was developed from scratch with usability, portability, and speed in mind from the start.

Bactopia uses Nextflow to manage the workflow, allowing for support of many types of environments (e.g. cluster or cloud). Bactopia allows for the usage of many public datasets as well as your own datasets to further enhance the analysis of your sequencing. Bactopia only uses software packages available from Bioconda and Conda-Forge to make installation as simple as possible for all users.

Funding

Support for this project came (in part) from an Emory Public Health Bioinformatics Fellowship funded by the CDC Emerging Infections Program, the Wyoming Public Health Division, the Center for Applied Pathogen Epidemiology and Outbreak Control (CAPE), and the CZI Open Science Program (EOSS6).

Citing Bactopia

Petit III RA, Read TD. Bactopia - a flexible pipeline for complete analysis of bacterial genomes. mSystems 5 (2020)