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 we (Tim Read and myself) released that targets 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 seqeuncing. Bactopia only uses software packages available from Bioconda (or other Anaconda channels) to make installation as simple as possible for all users.

To highlight the use of Bactopia Datasets, Bactopia, and Bactopia Tools, we performed an analysis of 1,664 public Lactobacillus genomes, focusing on Lactobacillus crispatus, a species that is a common part of the human vaginal microbiome. The results from this analysis are published in mSystems under the title: Bactopia: a flexible pipeline for complete analysis of bacterial genomes

Bactopia Workflow

Documentation Overview

Quick Start
Very concise and to straight the point details (unlike this!) for using Bactopia.

Installation
More detailed information for getting Bactopia set up on your system.

Basic Usage
A subset of parameters users may commonly adjust.

Tutorial
A brief tutorial on how to replicate the Staphopia Analysis Pipeline using Bactopia.

Build Datasets
A description on how to make use of datasets (public or private) with Bactopia.

Workflow Overview
A description of Bactopia workflow and software used.

Output Overview
A description of Bactopia output directories and files.

Complete Usage
The full set of parameters that users can tweak in Bactopia.

Acknowledgements
A list of datasets and software (and many thanks!) used by Bactopia.