BacPipe

BacPipe performs standardized analysis of bacterial whole-genome sequencing (WGS) data to support clinical diagnostic bacteriology, outbreak detection, and large-scale microbial surveillance.

Key Features:

• Support for input types: Direct analysis of bacterial WGS data from raw reads or contig files.
• Sequencing technologies: Compatible with second- and third-generation sequencing technologies, including Illumina paired-end reads.
• Standardization: Provides a pipeline approach that streamlines and standardizes bacterial WGS analyses for diagnostic and surveillance use.
• Scalability and throughput: Demonstrated ability to process large datasets, exemplified by processing 4,139 Illumina paired-end sequence files (genome sizes 2.9–5.4 Mb) from the European Nucleotide Archive.

Scientific Applications:

• Clinical diagnostic bacteriology: Enables standardized analysis of bacterial genomes for clinical diagnostic contexts.
• Outbreak detection: Supports genomic analyses used in detecting and investigating bacterial outbreaks.
• Public health surveillance and comparative genomics: Applicable to large-scale monitoring and comparative microbial genomics, including use in projects such as EBI-SELECTA under H2020-COMPARE.

Methodology:

Automated computational pipeline that processes raw reads or contigs derived from second- or third-generation sequencing (including Illumina paired-end) to produce standardized bacterial WGS analyses.