panmap

Pangenome-based sequence placement, alignment, and genotyping.

panmap takes sequencing reads and a pangenome in PanMAN format, places the reads onto the pangenome tree, aligns them to the closest reference, and calls variants.

At a glance

# Install
conda install -c bioconda panmap

# Place, genotype, and build consensus
panmap ref.panman reads_R1.fq reads_R2.fq -t 8 -o sample

# Metagenomic abundance estimation
panmap ref.panman reads.fq --meta --index ref.idx -t 8 -o sample

Modes

Single-sample (default)

Places reads from a single sample, aligns to the best-matching reference, and genotypes variants. Outputs BAM and VCF files.

Metagenomic (--meta)

Scores reads against every node in the PanMAN to estimate haplotype abundance or assign reads directly to nodes.

Documentation

• Installation – Bioconda, Docker, building from source
• Quick Start – Pipeline overview and basic examples
• Single-Sample Mode – Genotyping walkthrough
• Metagenomic Mode – Wastewater and aeDNA workflows
• CLI Reference – All options and flags

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