bactmap

What problem does it solve?

This Skill removes the guesswork from running the nf-core/bactmap pipeline so you can map bacterial whole-genome sequencing reads against a reference, produce reliable variant and pseudogenome outputs, and optionally generate a phylogeny from the resulting alignments.

Core Features & Use Cases

• Reference-based bacterial analysis: Runs a validated mapping workflow for short-read bacterial WGS data.
• Downstream interpretation: Produces filtered VCFs, pseudogenomes, and optional tree-building outputs for comparative genomics.
• Production-ready execution: Handles required parameters, runtime validation, version pinning, and provenance tracking for reproducible runs.

Quick Start

Ask me to run bactmap for your bacterial sequencing data by providing the reference genome, input sample information, output directory, and desired Nextflow profile.