panmap

CLI Reference

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

Use --help for common options or --help-all for the full list.

General

Option	Description	Default
-h, --help	Show common options	–
--help-all	Show all options	–
-V, --version	Show version	–
-o, --output	Output file prefix	derived from reads filename
-t, --threads	Number of threads	1
-a, --aligner	minimap2 or bwa	minimap2
--stop	Stop after: index, place, align, genotype, consensus	consensus
--meta	Enable metagenomic mode	off
-v, --verbose	Verbose output	off
-q, --quiet	Errors only	off
--no-color	Disable colored output	off

Index

Option	Description	Default
-i, --index	Path to pre-built index file	derived from output/panman
-f, --reindex	Force rebuild index	off
--index-mgsr	Build/rebuild MGSR index (metagenomic)	–
--index-full	Build full index instead of lite	off
--index-packed	Build packed Cap’n Proto message	off
--read-packed	Read packed Cap’n Proto message	off
--zstd-level	ZSTD compression level for index (1-22)	7

Seed parameters

Option	Description	Default
-k, --kmer	Syncmer k-mer length	19
-s, --syncmer	Syncmer s parameter	8
-l, --lmer	Syncmers per seed	3
--offset	Syncmer offset	0
--open-syncmer	Use open syncmers	off
--hpc	Homopolymer-compressed seeds	off
--flank-mask	Mask bp at ends of genomes	250
--seed-mask-fraction	Mask top seed fraction	0
--min-seed-quality	Minimum Phred score for seed region	0
--min-read-support	Minimum reads for a seed (2 = filter singletons)	1
--extent-guard	Guard seed deletions at genome extent boundaries	off

Read processing

Option	Description	Default
--trim-start	Trim bases from read start	0
--trim-end	Trim bases from read end	0
--dedup	Deduplicate reads	off

Placement

Option	Description	Default
--force-leaf	Restrict placement to leaf nodes (auto-enabled with --stop genotype)	off
--refine	Alignment-based refinement of top candidates	off
--refine-top-pct	Top fraction of nodes to refine	0.01
--refine-max-top-n	Max nodes to align against	150
--refine-neighbor-radius	Expand to neighbors within N branches	2
--refine-max-neighbor-n	Max additional nodes from neighbor expansion	150

Genotyping

Option	Description	Default
--impute	Impute N’s from parent (skip _->N mutations)	off
--no-mutation-spectrum	Disable mutation spectrum filtering in VCF	off
--baq	Enable Base Alignment Quality in mpileup	off

Metagenomic: EM algorithm

Option	Description	Default
--top-oc	Top N nodes by overlap coefficient to send to EM	1000
--mask-reads	Mask reads with k-min-mer total occurrence <= threshold	0
--mask-seeds	Mask k-min-mer seeds with total occurrence <= threshold	0
--amplicon-depth	Amplicon depth TSV for frequency-based masking	–
--mask-reads-relative-frequency	Mask reads with relative frequency < threshold * amplicon_depth	0.0
--mask-seeds-relative-frequency	Mask seeds with relative frequency < threshold * amplicon_depth	0.0
--em-convergence-threshold	Converge when likelihood difference < threshold	0.00001
--em-delta-threshold	Converge when max proportion change < threshold	0.0
--em-maximum-rounds	Maximum EM rounds	5
--em-maximum-iterations	Maximum EM iterations per round	1000
--em-leaves-only	Only run EM on leaf (sample) nodes	off
--no-progress	Disable progress bars	off

Metagenomic: filter and assign

Option	Description	Default
--filter-and-assign	Assign reads to nodes without EM	off
--dust	Discard reads with DUST score > threshold	100.0 (no filtering)
--discard	Discard reads with parsimony score < threshold * total seeds	0.0 (no discard)
--mask-read-ends	Mask N bases from read ends (for aeDNA damage)	0
--taxonomic-metadata	TSV with taxonomic metadata per node	–
--maximum-families	Discard reads spanning > N taxonomic families	1
--ambiguous-score-threshold-ratio	Discard reads scoring outside max families by ratio	0.0
--ambiguous-score-threshold	Discard reads scoring outside max families by absolute value	0
--breadth-ratio	Calculate observed/expected breadth ratio	off
--pseudochain	Use pseudo-chains for read scoring	off
--batch-files-path	TSV file containing batch file paths	–
--batch-size	Batch size for filtering and assigning	1000000

Batch mode

Option	Description	Default
--batch	File listing samples, one per line: reads1 [reads2] [output_prefix]	–

Utility

Option	Description
--dump-sequence <node>	Extract FASTA for a single node
--dump-sequences <nodes...>	Extract FASTA for multiple node IDs

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