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# 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.