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

annotate

Add or update genome metadata of an index from a CSV file, or dump the current metadata as CSV.

obikmer annotate INDEX --csv FILE [OPTIONS]
obikmer annotate INDEX --dump

Arguments

Argument Description
INDEX Index directory to annotate (modified in place)

Options

Option Default Description
--csv — CSV file of metadata to apply (must contain an id column); required unless --dump is used
--sep , CSV field separator
--id-col id Name of the column containing genome labels
--na-value NA Value meaning "remove this field" (deletes the existing key if present)
--no-overwrite off Do not overwrite existing metadata keys
--dump off Print all genome metadata as CSV to stdout instead of applying a file

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Theory

Kmer indexing

Phylogeny

Kmer-based

SNP-based

Usage

Formats