mash-sketch1
Create sketches (reduced representations for fast operations)
Usage
mash {sketch
[options]
fast(a | q)
[.gz] ...}
Overview
Create a sketch file, which is a reduced representation of a sequence or set of sequences (based on min-hashes) that can be used for fast distance estimations. Input can be fasta or fastq files (gzipped or not), and "-" can be given to read from standard input. Input files can also be files of file names (see -l). For output, one sketch file will be generated, but it can have multiple sketches within it, divided by sequences or files (see -i). By default, the output file name will be the first input file with a '.msh' extension, or 'stdin.msh' if standard input is used (see -o).
Options
-
-h -
Help
-
-p <int> -
Parallelism. This many threads will be spawned for processing. [1]
Input
-
-l -
List input. Each file contains a list of sequence files, one per line.
Output
-
-o <path> -
Output prefix (first input file used if unspecified). The suffix '.msh' will be appended.
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.
-
-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
-muses 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
-aor-z.
-
-a -
Use amino acid alphabet (A-Z, except BJOUXZ). Implies
-n,-k9.
-
-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.
Releases
5 releases since Debian 9 (Stretch); the text changed 3 times.