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Quick Start

Synopsis

panmap <panman> [reads1.fq] [reads2.fq] [options]

Pipeline

panmap runs five stages in sequence. By default it runs through consensus. Use --stop to stop earlier.

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

Single-sample genotyping

Place reads onto the pangenome, align to the closest reference, call variants, and generate a consensus:

panmap ref.panman reads_R1.fq reads_R2.fq -t 8 -o sample

This produces sample.bam, sample.vcf, and sample.consensus.fa.

Metagenomic abundance estimation

Estimate which lineages are present in a mixed sample:

panmap ref.panman reads.fq --meta -t 8 -o sample

Output: sample.mgsr.abundance.out

Partial pipelines

A plain run executes the full pipeline (place -> align -> genotype -> consensus) and writes .bam, .vcf, and .consensus.fa. Use --stop to end earlier:

# Stop at placement (writes .placement.tsv only)
panmap ref.panman reads.fq --stop place -o sample

# Place and align, skip genotyping and consensus
panmap ref.panman reads.fq --stop align -o sample

The --stop place/align/genotype/consensus stages are single-sample. With --meta, only --stop index applies (build the .midx and stop); the later stages don't run.

Managing indexes

panmap builds the index automatically on first run and reuses it after. The path is derived from the panman (not -o): a placement index at <panman>.idx and an MGSR index at <panman>.midx under --meta.

# Build the index only, next to the panman (no reads needed)
panmap ref.panman --stop index          # -> ref.panman.idx   (placement)
panmap ref.panman --meta --stop index   # -> ref.panman.midx  (metagenomic)

# Build to a custom path with --index-out (output), then load it with --index (input)
panmap ref.panman --stop index --index-out /data/ref.idx
panmap ref.panman reads.fq --index /data/ref.idx -o sample

# Force a rebuild
panmap ref.panman reads.fq --reindex -o sample

Next steps