hgtseq

What problem does it solve?

nf-core hgtseq automates a complex horizontal gene transfer analysis workflow so researchers do not have to manually stitch together preprocessing, alignment, taxonomic screening, and reporting steps.

Core Features & Use Cases

• Reproducible release-pinned execution of the hgtseq pipeline.
• Validated sample sheet and required parameters for reliable runs.
• Built-in output organization, MultiQC reporting, and provenance capture.
• Use case: a bioinformatics researcher can analyze sequencing data for suspected horizontal gene transfer and generate a standardized results directory for review and sharing.

Quick Start

Ask the agent to run hgtseq on my samplesheet with the required taxonomy ID, output directory, and reference databases, then produce the pipeline results and report.