panmap

Pangenome-based sequence placement, alignment, and genotyping.

panmap takes sequencing reads and a pangenome in PanMAN format, places each sample onto the pangenome, and then either aligns and genotypes it against the closest reference (single-sample mode) or estimates haplotype abundances and assigns reads to pangenome nodes (metagenomic mode).

At a glance

# Install
conda install -c conda-forge -c bioconda panmap

# Place, genotype, and build a consensus (single-sample, default)
panmap ref.panman reads_R1.fq reads_R2.fq -t 8 -o sample

# Estimate haplotype abundances from a mixture (metagenomic)
panmap ref.panman reads.fq --meta -t 8 -o sample

Modes

Single-sample (default)

Places reads from a single sample, aligns to the best-matching reference, and genotypes variants. Produces a placement, BAM, VCF, and consensus FASTA.

Metagenomic (--meta)

Scores reads against every node in the PanMAN to estimate haplotype abundance, or assigns reads directly to nodes for taxonomic identification.

Documentation

• Installation

  Bioconda, Docker, and building from source.

• Quick Start

  Pipeline overview and basic examples.

• Single-Sample Mode

  Genotyping walkthrough.

• Metagenomic Mode

  Wastewater and aeDNA workflows.

• Outputs

  Every file panmap writes.

• CLI Reference

  All options and flags.

Citing panmap

If you use panmap, please cite the preprint:

panmap: pangenome-based sequence placement, alignment, and genotyping. bioRxiv 10.64898/2026.03.29.711974.