Positional arguments:¶

files

Input sequence files [nargs: 0 or more] [required]

Optional arguments:¶

-v, --version prints version information and exits

-k

k-mer size [required]

-o

Output file (for -f collect) or directory path [required]

-f

Output file organization (store hashes for each 'file', 'record', or 'collect' all hashes into a single file [default: "file"]

-h

Number of hashes per k-mer/seed [default: 1]

-s

Input spaced seed patterns separated by commas (e.g. 1110111,11011011). Performs k-mer hashing if no value provided.

--long

Optimize file reader for long sequences (>5kbp)

--binary

Output hashes in binary files (otherwise plain text)

--verbose

Print progress to stdout