panmap <panman> [reads1.fq] [reads2.fq] [options]
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
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.
Estimate which lineages are present in a mixed sample:
# Build metagenomic index (once per pangenome)
panmap ref.panman --index-mgsr ref.idx
# Estimate abundances
panmap ref.panman reads.fq \
--meta --index ref.idx -t 8 -o sample
Output: sample.mgsr.abundance.out
# Build index only
panmap ref.panman --stop index -o ref
# Place reads (default)
panmap ref.panman reads.fq -o sample
# Place and align, skip genotyping
panmap ref.panman reads.fq --stop align -o sample