28 lines
1.2 KiB
Markdown
28 lines
1.2 KiB
Markdown
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# superkmer
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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.
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```bash
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obikmer superkmer [OPTIONS] [INPUTS...]
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```
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## Arguments
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| Argument | Description |
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|---|---|
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| `INPUTS...` | Input sequence files or directories (FASTA/FASTQ/GenBank, gzip optional). If omitted, reads from stdin. |
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## Options
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| Option | Default | Description |
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|---|---|---|
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| `-k, --kmer-size` | `31` | Kmer size (must be odd, in [11, 31]) |
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| `-m, --minimizer-size` | `11` | Minimizer size (must be odd, in $[3, k-1]$) |
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| `--theta` | `0.7` | Entropy threshold; kmers with a normalized entropy at or below this value are excluded |
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| `--level-max` | `6` | Maximum sub-word size used for the entropy score |
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| `-p, --partitions` | `256` | Number of partitions (rounded up to the next power of 2) |
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| `-T, --threads` | detected core count | Number of worker threads |
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| `--max-open-files` | `threads / 4` (min 1) | Maximum number of input files open simultaneously |
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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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