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

utils

Miscellaneous index maintenance and inspection utilities.

obikmer utils INDEXES... [OPTIONS]

Arguments

Argument Description
INDEXES... One or more index directories

Options

Option Scope Description
--new-label NEW=OLD single index only Rename a genome label
--upgrade-index single index only Add any missing layer metadata files to an older index
--bits-per-kmer single index only Print bits-per-kmer statistics
--stats single index only Print per-genome kmer counts as CSV
--partition-stats one or more indexes Print a partition-size distribution report
--csv FILE with --partition-stats Also write raw per-(partition, source) data to FILE as CSV

At least one operation option must be given. All options except --partition-stats require exactly one index directory.

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Theory

Kmer indexing

Phylogeny

Kmer-based

SNP-based

Usage

Formats