PeGAS: a versatile bioinformatics pipeline for antimicrobial resistance, virulence and pangenome analysis.

Motivation: Antimicrobial resistance is increasingly recognized as one of the most significant global health threats, with profound implications for human, animal, and environmental health. Genome analysis represents a very useful tool that provides accurate and reproducible results allowing for the advancement of knowledge regarding antimicrobial resistance diagnosis, therapeutics, surveillance, transmission, and evolution. However, due to increasing complexity of bacterial genome analysis and computational power required for genomic approaches, there is a continuous need for comprehensive, user-friendly tools for data analysis. We developed Pangenome and Genomic Analysis Suite (PeGAS), to address some of these challenges by offering an all-in-one pipeline that performs a range of analyses. Results: PeGAS integrates key genomic analysis features of bacteria whole genome sequencing, including the prediction of antimicrobial resistance profiles, sorted by various categories of antibiotics, VF detection, and plasmid replicon assignment. The pipeline also performs pangenome analysis, multilocus sequence typing, genome assembly quality control (by reporting statistics such as GC content, contig length, the number of contigs, as well as variation from certain GC thresholds) providing a comprehensive genomic overview. PeGAS also offers the ability to restart seamlessly from any sporadic interruptions that might occur during long or resource-intensive runs. Availability and implementation: PeGAS is available at: https://github.com/liviurotiul/PeGAS.