panmap

Pangenome-based sequence placement, alignment, and genotyping.

Documentation | Preprint

Install

docker pull alanalohaucsc/panmap:latest

Quick start

# Place and genotype paired-end reads
panmap ref.panman reads_R1.fq reads_R2.fq -t 8 -o sample

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

Pipeline

index  -->  place  -->  align  -->  genotype  -->  consensus
 .idx    .placement.tsv  .bam       .vcf        .consensus.fa

By default, panmap stops after placement. Use --stop to run further stages.

Modes

• Single-sample (default): Place reads, align to closest reference, call variants (BAM + VCF)
• Metagenomic (--meta): Estimate haplotype abundance or assign reads to pangenome nodes

Links

• Full documentation
• Installation options
• CLI reference
• PanMAN format