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usage merge

Eric Coissac edited this page 2026-09-12 14:00:23 +02:00

Table of Contents

• merge
• Arguments
• Options
• Behaviour

merge

Merge multiple built indexes into a single index.

obikmer merge -o OUTPUT SOURCE... [OPTIONS]

Arguments

Argument	Description
SOURCE...	Index directories to merge (at least one required)

Options

Option	Default	Description
-o, --output	— (required)	Output index directory
--force	off	Overwrite an existing output directory
--force-presence	off	Store the merged index as presence/absence even if all sources have counts
--rename-duplicates	off	Disambiguate duplicate genome labels (.1, .2, …) instead of failing
--budget-fraction	0.5	Fraction of available RAM reserved as the memory budget for parallel partition merging

Behaviour

The output mode is chosen automatically: if every source index stores counts, the merged index stores counts too; otherwise it is presence/absence. --force-presence forces presence/absence regardless of the sources.

By default, merging two indexes that share a genome label fails with an error; --rename-duplicates instead appends a numeric suffix to keep both copies.

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Theory

Kmer indexing

• DNA encoding
• Kmers
• Minimizer selection
• Super-kmers
• Partitioning and indexing architecture
• Low-complexity kmer filter

Phylogeny

Kmer-based

• Whole k-mer set distances

SNP-based

• Central-position SNP model
• Gamma rate heterogeneity
• Sankoff model
• Sampling design

Usage

• superkmer
• index
• merge
• filter
• select
• query
• dump
• annotate
• phylo
• unitig
• estimate
• convert
• utils
• pack
• Predicates and taxonomy paths

Formats

• Index construction and on-disk layout
• Architecture notes