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

estimate

Estimate approximate-index parameters (z, evidence bits, false-positive rate) before building an index with --approx, without touching any files.

obikmer estimate [OPTIONS]

Options

Option Default Description
-k, --kmer-size 31 Kmer size used at query time (matches index's --kmer-size)
-z, --findere-z none Findere z parameter
--evidence-bits none Fingerprint bits per slot (b)
--fp none Target false-positive rate per z-window

Any two of -z, --evidence-bits, --fp may be given; the third is derived using the same model as index --approx and convert --approx-evidence (FP = 1 / 2^{b \cdot z}). The report printed to stdout includes: query k, effective indexed k (k-z+1), z, evidence bits, per-kmer false-positive rate, and per-z-window false-positive rate.

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Theory

Kmer indexing

Phylogeny

Kmer-based

SNP-based

Usage

Formats