-h
Help
-p <int>
Parallelism. This many threads will be spawned for
processing. [1]
-l
List input. Each query file contains a list of sequence
files, one per line. The reference file is not affected.
-C
Use comment fields for sequence names instead of
IDs.
-E
Output edge list instead of Phylip matrix, with fields
[seq1, seq2, dist, p-val, shared-hashes].
-v <num>
Maximum p-value to report in edge list. Implies -E. (0-1)
[1.0]
-d <num>
Maximum distance to report in edge list. Implies -E.
(0-1) [1.0]
-k <int>
K-mer size. Hashes will be based on strings of this many
nucleotides. Canonical nucleotides are used by default (see Alphabet options
below). (1-32) [21]
-s <int>
Sketch size. Each sketch will have at most this many
non-redundant min-hashes. [1000]
-i
Sketch individual sequences, rather than whole files,
e.g. for multi-fastas of single-chromosome genomes or pair-wise gene
comparisons.
-w <num>
Probability threshold for warning about low k-mer size.
(0-1) [0.01]
-r
Input is a read set. See Reads options below.
Incompatible with -i.
-b <size>
Use a Bloom filter of this size (raw bytes or with
K/M/G/T) to filter out unique k-mers. This is useful if exact filtering with
-m uses too much memory. However, some unique k-mers may pass
erroneously, and copies cannot be counted beyond 2. Implies -r.
-m <int>
Minimum copies of each k-mer required to pass noise
filter for reads. Implies -r. [1]
-c <num>
Target coverage. Sketching will conclude if this coverage
is reached before the end of the input file (estimated by average k-mer
multiplicity). Implies -r.
-g <size>
Genome size. If specified, will be used for p-value
calculation instead of an estimated size from k-mer content. Implies
-r.
-n
Preserve strand (by default, strand is ignored by using
canonical DNA k-mers, which are alphabetical minima of forward-reverse pairs).
Implied if an alphabet is specified with -a or -z.
-a
Use amino acid alphabet (A-Z, except BJOUXZ). Implies
-n, -k 9.
-z <text>
Alphabet to base hashes on (case ignored by default; see
-Z). K-mers with other characters will be ignored. Implies
-n.
-Z
Preserve case in k-mers and alphabet (case is ignored by
default). Sequence letters whose case is not in the current alphabet will be
skipped when sketching.