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Bactopia: a Flexible Pipeline for Complete Analysis of Bacterial Genomes. | LitMetric

Bactopia: a Flexible Pipeline for Complete Analysis of Bacterial Genomes.

mSystems

Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA

Published: August 2020

AI Article Synopsis

  • Bactopia is a new series of pipelines developed using Nextflow software that streamlines comparative genomic analyses for bacterial species, enabling users to efficiently manage data from Illumina sequencing.
  • The pipeline consists of three main components: Bactopia Data Sets (BaDs) for custom data setup, the Bactopia Analysis Pipeline (BaAP) for quality control and genome assembly, and Bactopia Tools (BaTs) for specialized postprocessing tasks like pan-genome analysis and taxonomic classification.
  • Bactopia is open source, scalable for small or large projects, and simplifies the bioinformatic analysis of bacterial genomes by integrating multiple software tools and automating data downloads from public sources.

Article Abstract

Sequencing of bacterial genomes using Illumina technology has become such a standard procedure that often data are generated faster than can be conveniently analyzed. We created a new series of pipelines called Bactopia, built using Nextflow workflow software, to provide efficient comparative genomic analyses for bacterial species or genera. Bactopia consists of a data set setup step (Bactopia Data Sets [BaDs]), which creates a series of customizable data sets for the species of interest, the Bactopia Analysis Pipeline (BaAP), which performs quality control, genome assembly, and several other functions based on the available data sets and outputs the processed data to a structured directory format, and a series of Bactopia Tools (BaTs) that perform specific postprocessing on some or all of the processed data. BaTs include pan-genome analysis, computing average nucleotide identity between samples, extracting and profiling the 16S genes, and taxonomic classification using highly conserved genes. It is expected that the number of BaTs will increase to fill specific applications in the future. As a demonstration, we performed an analysis of 1,664 public genomes, focusing on , a species that is a common part of the human vaginal microbiome. Bactopia is an open source system that can scale from projects as small as one bacterial genome to ones including thousands of genomes and that allows for great flexibility in choosing comparison data sets and options for downstream analysis. Bactopia code can be accessed at https://www.github.com/bactopia/bactopia It is now relatively easy to obtain a high-quality draft genome sequence of a bacterium, but bioinformatic analysis requires organization and optimization of multiple open source software tools. We present Bactopia, a pipeline for bacterial genome analysis, as an option for processing bacterial genome data. Bactopia also automates downloading of data from multiple public sources and species-specific customization. Because the pipeline is written in the Nextflow language, analyses can be scaled from individual genomes on a local computer to thousands of genomes using cloud resources. As a usage example, we processed 1,664 genomes from public sources and used comparative analysis workflows (Bactopia Tools) to identify and analyze members of the species.

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7406220PMC
http://dx.doi.org/10.1128/mSystems.00190-20DOI Listing

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