BacPipe

"BacPipe" is a comprehensive and computationally efficient bioinformatics pipeline for analyzing bacterial whole-genome sequences (WGS) derived from second or third-generation sequencing technologies. Recognizing the challenges in integrating WGS technologies into routine microbiological diagnostics, BacPipe aims to standardize the downstream bioinformatics analysis, making it more accessible for hospitals, public health initiatives, and infection control monitoring.

Key Features and Functionalities:

- Comprehensive WGS Analysis: BacPipe enables direct analyses of raw reads or contigs from bacterial whole-genome sequences, offering a broad range of analytical capabilities to accommodate the needs of microbiological diagnostics.

- Graphical User Interface: A user-friendly graphical interface is developed to visualize the real-time progression of the analysis, enhancing the usability of the pipeline for users with varying levels of bioinformatics expertise.

- Scalability and Speed: Demonstrated to handle large datasets efficiently, BacPipe's scalability and speed were validated using 4,139 Illumina paired-end sequence files of bacterial genomes from the European Nucleotide Archive, covering genomes ranging from 2.9 to 5.4 Mb.

- Integration in EBI-SELECTA: BacPipe is integrated within EBI-SELECTA, a project-specific portal developed under the H2020-COMPARE project, facilitating its accessibility and application in broader research and diagnostic projects.

- Availability as an Independent Docker Image: To ensure compatibility across different operating systems, BacPipe is available as an independent docker image that can be used on both Windows- and Unix-based systems, simplifying installation and deployment.

- Automated "One-Stop" Analysis: Offering a fully automated pipeline, BacPipe serves as a "one-stop" solution for bacterial WGS analysis, addressing the major bottleneck of WGS data analysis in clinical and public health contexts: identification, antimicrobial resistance detection, and epidemiological monitoring.