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]
-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.
