BacWGSpipe: A Snakemake Workflow for a Complete Analysis of Bacterial Whole-Genome Sequencing Data

Whole-genome sequencing (WGS) provides a comprehensive view of the bacterial genome, enabling the identification of genetic determinants associated with antibiotic resistance, virulence, and other key clinical traits. Translating WGS data into the clinic requires a diverse collection of bioinformatics tools. Effectively using these analysis tools in a scalable and reproducible way can be challenging, especially for non-experts. We have developed the BacWGSpipe, an automated, scalable, reproducible, and open-source framework for bacterial genomics using WGS data from Illumina, PacBio and Nanopore platforms. BacWGSpipe combines some state-of-the-art tools to take genomic analysis from raw sequencing data through quality control, de novo genome assembly, genotyping, gene annotation and functional analysis, antimicrobial resistance (AMR), virulence and mobile genetic elements profiling, in addition to pangenome analysis, phylogenetic reconstruction and single-nucleotide polymorphism (SNP) variant calling. Once the analysis is finished, BacWGSpipe generates an interactive web-like html report. Using Snakemake and Conda, BacWGSpipe can be easily installed to any computation environment.