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usage dump
Eric Coissac edited this page 2026-09-12 14:00:23 +02:00
Table of Contents

dump

Dump all kmers of an index as CSV, one row per kmer, with per-genome counts or presence.

obikmer dump INDEX [OPTIONS]

Arguments

Argument Description
INDEX Index directory to dump

Options

Option Default Description
--force-presence off Output presence/absence (0/1) even if the index stores counts
--debug off Prefix each row with the partition and layer columns
--head N none Limit output to the first N kmers

dump also accepts the shared predicate options (--ingroup, --outgroup, --min-count, etc.) to restrict which kmers are dumped.

Output is CSV on stdout.

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Theory

Kmer indexing

Phylogeny

Kmer-based

SNP-based

Usage

Formats