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.