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

superkmer

Extract super-kmers from one or more sequence files and write them to stdout, without building a full index. Useful for inspecting or piping the super-kmer decomposition of a dataset.

obikmer superkmer [OPTIONS] [INPUTS...]

Arguments

Argument Description
INPUTS... Input sequence files or directories (FASTA/FASTQ/GenBank, gzip optional). If omitted, reads from stdin.

Options

Option Default Description
-k, --kmer-size 31 Kmer size (must be odd, in [11, 31])
-m, --minimizer-size 11 Minimizer size (must be odd, in [3, k-1])
--theta 0.7 Entropy threshold; kmers with a normalized entropy at or below this value are excluded
--level-max 6 Maximum sub-word size used for the entropy score
-p, --partitions 256 Number of partitions (rounded up to the next power of 2)
-T, --threads detected core count Number of worker threads
--max-open-files threads / 4 (min 1) Maximum number of input files open simultaneously

Output is written to stdout in the internal scatter format used by index; it is primarily intended to be piped into other tools or inspected for debugging.

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Theory

Kmer indexing

Phylogeny

Kmer-based

SNP-based

Usage

Formats