hgtseq

hgtseq analyzes exome and whole-genome sequencing data to detect and characterize horizontal gene transfer (HGT) events across diverse organisms.

Key Features:

• Nextflow integration: Implements workflows using Nextflow to orchestrate the analysis pipeline.
• nf-core standards: Adheres to nf-core specifications to enforce reproducibility and standardized pipeline structure.
• Automation: Executes automated processing steps to identify candidate HGT events from sequencing data.
• Portability and scalability: Supports execution across different computing environments and scales with available resources.
• Input compatibility: Accepts high-throughput exome and whole-genome sequencing datasets as input for HGT analysis.
• Comparative analysis support: Enables comparative analyses of HGT across multiple samples and species.

Scientific Applications:

• Prokaryote and eukaryote HGT studies: Investigates the mechanisms and extent of HGT in prokaryotes, insects, plants, and other eukaryotes.
• Human sequencing analyses: Detects microbial sequences and reports of bacterial integrations in human sequencing datasets, including cancer samples.
• Mammalian comparative studies: Facilitates standardized analysis across mammalian exome datasets, as demonstrated on six exome datasets from five mammalian subjects.

Methodology:

hgtseq uses Nextflow workflows implemented to nf-core standards to process exome and whole-genome sequencing data for detection and comparative analysis of HGT events.