mash-triangle1

Input

-l

List input. Each query file contains a list of sequence files, one per line. The reference file is not affected.

Output

-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]

Sketching

-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.

Sketching (reads)

-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.

Sketching (alphabet)

-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.