NAME
mash-sketch - create sketches (reduced representations for fast operations)
SYNOPSIS
mash sketch [options] fast(a|q)[.gz] ...
DESCRIPTION
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 -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.