Bactopia

Bactopia performs automated processing and comparative analysis of bacterial genomes from Illumina sequence data, providing quality control, genome assembly, and downstream comparative and taxonomic analyses using Nextflow.

Key Features:

• Bactopia Data Sets (BaDs): Configurable data set setup tailored to specific species or genera for organization and preparation of input data.
• Bactopia Analysis Pipeline (BaAP): Executes quality control checks, genome assembly, and other preprocessing tasks and organizes outputs into a structured directory format.
• Bactopia Tools (BaTs): Provides postprocessing functions including pan-genome analysis, average nucleotide identity computation, 16S gene extraction and profiling, and taxonomic classification using highly conserved genes.
• Nextflow workflow management: Implements workflows using the Nextflow language for scalable execution and reproducible pipeline orchestration.
• Scalability and customization: Supports projects from single genomes to thousands of genomes and allows species-specific customizations and integration of data from multiple public sources.
• Sequencing technology support: Supports input from Illumina sequencing data for downstream processing and analysis.

Scientific Applications:

• Comparative genomics: Enables comparative analyses across multiple bacterial genomes to identify species- or clade-specific characteristics.
• Pan-genome analysis: Facilitates construction and analysis of pan-genomes from assembled genomes.
• Taxonomic classification: Performs taxonomic classification using highly conserved genes and 16S profiling.
• Average Nucleotide Identity (ANI): Computes ANI between samples for genomic similarity and species delineation.
• 16S gene extraction and profiling: Extracts and profiles 16S genes from assemblies for taxonomic and community analyses.
• Large-scale genome surveys: Has been applied to analyze thousands of genomes, exemplified by analyses of 1,664 publicly available Lactobacillus genomes including Lactobacillus crispatus.

Methodology:

Uses Bactopia Data Sets (BaDs) to prepare input, runs the Bactopia Analysis Pipeline (BaAP) for quality control, genome assembly and preprocessing, organizes outputs into structured directories, and applies Bactopia Tools (BaTs) for pan-genome analysis, average nucleotide identity computation, 16S gene extraction and profiling, and taxonomic classification under Nextflow workflow management.