MicroPIPE

MicroPIPE assembles high-quality bacterial genomes by integrating ONT long reads and Illumina short reads for accurate microbial genome reconstruction.

Key Features:

• Integration of ONT and Illumina Sequencing: Combines ONT long reads with Illumina short reads to achieve comprehensive coverage and precise bacterial genome assembly.
• Reproducibility and Automation: Uses Singularity containers to ensure consistent computational environments and reproducible execution.
• Workflow Management with Nextflow: Employs Nextflow for workflow orchestration, enabling parallel processing and resource management.
• Comprehensive Validation: Validated using diverse bacterial isolates including 11 sequence type (ST)131 Escherichia coli strains and eight additional publicly available Gram-negative and Gram-positive bacteria.

Scientific Applications:

• Microbial genome assembly: Produces accurate and complete bacterial genomes for downstream analyses.
• Phylogenetic studies: Provides high-quality assemblies suitable for comparative and phylogenetic analyses.
• Pathogen surveillance: Enables generation of complete genomes for tracking and surveillance of pathogens.
• Antimicrobial resistance profiling: Facilitates detection and analysis of resistance determinants from accurate genome sequences.

Methodology:

Evaluated multiple genome reconstruction tools by assessing their accuracy and efficiency on ONT data alone and ONT data supplemented with Illumina reads.