Bactopia: a Flexible Pipeline for Complete Analysis of Bacterial Genomes

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 comparati...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Robert A. Petit, Timothy D. Read
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2020
Materias:	annotation assembly bacteria genomics Lactobacillus software Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/a758e480a17348c4a30a7dfee665d185
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:a758e480a17348c4a30a7dfee665d185
record_format	dspace
spelling	oai:doaj.org-article:a758e480a17348c4a30a7dfee665d1852021-12-02T18:44:37ZBactopia: a Flexible Pipeline for Complete Analysis of Bacterial Genomes10.1128/mSystems.00190-202379-5077https://doaj.org/article/a758e480a17348c4a30a7dfee665d1852020-08-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSystems.00190-20https://doaj.org/toc/2379-5077ABSTRACT 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 Lactobacillus genomes, focusing on Lactobacillus crispatus, 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. IMPORTANCE 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 Lactobacillus genomes from public sources and used comparative analysis workflows (Bactopia Tools) to identify and analyze members of the L. crispatus species.Robert A. PetitTimothy D. ReadAmerican Society for MicrobiologyarticleannotationassemblybacteriagenomicsLactobacillussoftwareMicrobiologyQR1-502ENmSystems, Vol 5, Iss 4 (2020)
institution	DOAJ
collection	DOAJ
language	EN
topic	annotation assembly bacteria genomics Lactobacillus software Microbiology QR1-502
spellingShingle	annotation assembly bacteria genomics Lactobacillus software Microbiology QR1-502 Robert A. Petit Timothy D. Read Bactopia: a Flexible Pipeline for Complete Analysis of Bacterial Genomes
description	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 Lactobacillus genomes, focusing on Lactobacillus crispatus, 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. IMPORTANCE 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 Lactobacillus genomes from public sources and used comparative analysis workflows (Bactopia Tools) to identify and analyze members of the L. crispatus species.
format	article
author	Robert A. Petit Timothy D. Read
author_facet	Robert A. Petit Timothy D. Read
author_sort	Robert A. Petit
title	Bactopia: a Flexible Pipeline for Complete Analysis of Bacterial Genomes
title_short	Bactopia: a Flexible Pipeline for Complete Analysis of Bacterial Genomes
title_full	Bactopia: a Flexible Pipeline for Complete Analysis of Bacterial Genomes
title_fullStr	Bactopia: a Flexible Pipeline for Complete Analysis of Bacterial Genomes
title_full_unstemmed	Bactopia: a Flexible Pipeline for Complete Analysis of Bacterial Genomes
title_sort	bactopia: a flexible pipeline for complete analysis of bacterial genomes
publisher	American Society for Microbiology
publishDate	2020
url	https://doaj.org/article/a758e480a17348c4a30a7dfee665d185
work_keys_str_mv	AT robertapetit bactopiaaflexiblepipelineforcompleteanalysisofbacterialgenomes AT timothydread bactopiaaflexiblepipelineforcompleteanalysisofbacterialgenomes
_version_	1718377697090994176

Bactopia: a Flexible Pipeline for Complete Analysis of Bacterial Genomes

Ejemplares similares