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 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.

Characterization of the first vaginal Lactobacillus crispatus genomes isolated in Brazil

“…2 ), lacking one or more domains. Also, the subtype II-C in CRI10 is probably a prediction artifact, as a single subtype with two sets of cas genes can be detected as multiple subtypes ( Crawley et al, 2018 ) and only the subtypes I-B, I-E, and II-A were reported for this species ( Petit & Read, 2020 ). The result suggests that the CRISPR-Cas systems are not functional due to gene fragmentation which could compromise the prevention of phage infections.…”

“…Comparative genomic analyses have been performed to identify genomic features of L. crispatus associated with female urogenital tract using samples from North America, Europe and Asia ( Ojala et al, 2014 ; Abdelmaksoud et al, 2016 ; France, Mendes-Soares & Forney, 2016 ; Van der Veer et al, 2019 ; Pan, Hidalgo-Cantabrana & Barrangou, 2020 ; Petit & Read, 2020 ; Zhang et al, 2020 ). Analyses that searched for genomic features associated with lactobacilli-dominated (healthy) or BV microbiota were performed using samples isolated from the USA ( Abdelmaksoud et al, 2016 ) and Netherlands ( Van der Veer et al, 2019 ).…”

Pelistega ratti sp. nov. from Rattus norvegicus of Hainan island

“…ezbiocloud. net/ tools/ ani) [28] revealed that the ANI values of strains NLN63 T and NLN82 were lower than the threshold (95-96 %) with other recognized species in genus Pelistega ( Table 2). Of note, the ANI value between strains NLN63 T and NLN82 was 98.1 %, above the threshold, indicating that they belong to the same species.…”

“…Overall genome relatedness indices, especially average nucleotide identity (ANI), have been increasingly used [23–27]. ANI calculation applied in this study to delineate species using the OrthoANIu algorithm (www.ezbiocloud.net/tools/ani) [28] revealed that the ANI values of strains NLN63 T and NLN82 were lower than the threshold (95–96 %) with other recognized species in genus Pelistega (). Of note, the ANI value between strains NLN63 T and NLN82 was 98.1 %, above the threshold, indicating that they belong to the same species.…”

MicroPIPE: An end-to-end solution for high-quality complete bacterial genome construction

“…Numerous tools designed to address aspects of complete bacterial genome construction have been developed by both ONT and community users, however few pipelines exist that offer end-to-end construction of bacterial genomes. Currently, these include Katuali (ONT), CCBGpipe [4], ASA 3 P [5] and Bactopia [6]. Katuali is an ONT developed assembly pipeline implemented in Snakemake.…”