CholeraSeq

CholeraSeq provides a high-throughput Nextflow pipeline for genomic surveillance of cholera outbreaks, unifying read quality control, filtering, reference mapping, variant calling, annotation, recombination screening, extraction of parsimony informative sites and variant codons, and phylogenetic inference to accelerate outbreak investigation and public health response.

Key Features:

• Multi-input compatibility: The pipeline ingests consensus genomes, short read sequence data, and draft assemblies.
• Comprehensive variant analysis: It performs read QC, filtering, reference mapping, variant calling, variant annotation, recombination screening, and extraction of parsimony informative sites and variant codons.
• Phylogenetic inference: It generates phylogenies for downstream phylodynamic and epidemiological analyses.
• Curated reference alignment: A ready-to-use core genome alignment compiled from public data enables flexible, fast integration of new samples for outbreak investigations.
• Scalable architecture: The pipeline scales seamlessly from local to cloud environments and is implemented with a modular design building upon nf-core community standards.

Scientific Applications:

• Cholera genomic surveillance: The pipeline supports systematic monitoring of Vibrio cholerae populations for public health tracking.
• Near real-time outbreak investigation: It accelerates epidemiological context placement of new outbreak strains to speed public health response.
• Phylodynamic analysis: Generated phylogenies enable downstream phylodynamic and epidemiological analyses of outbreak dynamics.

Methodology:

CholeraSeq is implemented in Nextflow with a modular design building upon nf-core community standards. The pipeline performs read quality control, filtering, reference mapping, variant calling, variant annotation, recombination screening, extraction of parsimony informative sites and variant codons, and phylogenetic inference.