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annotate CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/share/man/man1/mash-sketch.1 @ 68:5028fdace37b

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planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
author jpayne
date Tue, 18 Mar 2025 16:23:26 -0400
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jpayne@68 1 '\" t
jpayne@68 2 .\" Title: mash-sketch
jpayne@68 3 .\" Author: [see the "AUTHOR(S)" section]
jpayne@68 4 .\" Generator: Asciidoctor 2.0.10
jpayne@68 5 .\" Date: 2019-12-13
jpayne@68 6 .\" Manual: \ \&
jpayne@68 7 .\" Source: \ \&
jpayne@68 8 .\" Language: English
jpayne@68 9 .\"
jpayne@68 10 .TH "MASH\-SKETCH" "1" "2019-12-13" "\ \&" "\ \&"
jpayne@68 11 .ie \n(.g .ds Aq \(aq
jpayne@68 12 .el .ds Aq '
jpayne@68 13 .ss \n[.ss] 0
jpayne@68 14 .nh
jpayne@68 15 .ad l
jpayne@68 16 .de URL
jpayne@68 17 \fI\\$2\fP <\\$1>\\$3
jpayne@68 18 ..
jpayne@68 19 .als MTO URL
jpayne@68 20 .if \n[.g] \{\
jpayne@68 21 . mso www.tmac
jpayne@68 22 . am URL
jpayne@68 23 . ad l
jpayne@68 24 . .
jpayne@68 25 . am MTO
jpayne@68 26 . ad l
jpayne@68 27 . .
jpayne@68 28 . LINKSTYLE blue R < >
jpayne@68 29 .\}
jpayne@68 30 .SH "NAME"
jpayne@68 31 mash\-sketch \- create sketches (reduced representations for fast operations)
jpayne@68 32 .SH "SYNOPSIS"
jpayne@68 33 .sp
jpayne@68 34 \fBmash sketch\fP [options] fast(a|q)[.gz] ...
jpayne@68 35 .SH "DESCRIPTION"
jpayne@68 36 .sp
jpayne@68 37 Create a sketch file, which is a reduced representation of a sequence or set
jpayne@68 38 of sequences (based on min\-hashes) that can be used for fast distance
jpayne@68 39 estimations. Input can be fasta or fastq files (gzipped or not), and "\-" can
jpayne@68 40 be given to read from standard input. Input files can also be files of file
jpayne@68 41 names (see \fB\-l\fP). For output, one sketch file will be generated, but it can have
jpayne@68 42 multiple sketches within it, divided by sequences or files (see \fB\-i\fP). By
jpayne@68 43 default, the output file name will be the first input file with a \(aq.msh\(aq
jpayne@68 44 extension, or \(aqstdin.msh\(aq if standard input is used (see \fB\-o\fP).
jpayne@68 45 .SH "OPTIONS"
jpayne@68 46 .sp
jpayne@68 47 \fB\-h\fP
jpayne@68 48 .RS 4
jpayne@68 49 Help
jpayne@68 50 .RE
jpayne@68 51 .sp
jpayne@68 52 \fB\-p\fP <int>
jpayne@68 53 .RS 4
jpayne@68 54 Parallelism. This many threads will be spawned for processing. [1]
jpayne@68 55 .RE
jpayne@68 56 .SS "Input"
jpayne@68 57 .sp
jpayne@68 58 \fB\-l\fP
jpayne@68 59 .RS 4
jpayne@68 60 List input. Each file contains a list of sequence files, one per line.
jpayne@68 61 .RE
jpayne@68 62 .SS "Output"
jpayne@68 63 .sp
jpayne@68 64 \fB\-o\fP <path>
jpayne@68 65 .RS 4
jpayne@68 66 Output prefix (first input file used if unspecified). The suffix
jpayne@68 67 \(aq.msh\(aq will be appended.
jpayne@68 68 .RE
jpayne@68 69 .SS "Sketching"
jpayne@68 70 .sp
jpayne@68 71 \fB\-k\fP <int>
jpayne@68 72 .RS 4
jpayne@68 73 K\-mer size. Hashes will be based on strings of this many
jpayne@68 74 nucleotides. Canonical nucleotides are used by default (see
jpayne@68 75 Alphabet options below). (1\-32) [21]
jpayne@68 76 .RE
jpayne@68 77 .sp
jpayne@68 78 \fB\-s\fP <int>
jpayne@68 79 .RS 4
jpayne@68 80 Sketch size. Each sketch will have at most this many non\-redundant
jpayne@68 81 min\-hashes. [1000]
jpayne@68 82 .RE
jpayne@68 83 .sp
jpayne@68 84 \fB\-i\fP
jpayne@68 85 .RS 4
jpayne@68 86 Sketch individual sequences, rather than whole files.
jpayne@68 87 .RE
jpayne@68 88 .sp
jpayne@68 89 \fB\-w\fP <num>
jpayne@68 90 .RS 4
jpayne@68 91 Probability threshold for warning about low k\-mer size. (0\-1) [0.01]
jpayne@68 92 .RE
jpayne@68 93 .sp
jpayne@68 94 \fB\-r\fP
jpayne@68 95 .RS 4
jpayne@68 96 Input is a read set. See Reads options below. Incompatible with \fB\-i\fP.
jpayne@68 97 .RE
jpayne@68 98 .SS "Sketching (reads)"
jpayne@68 99 .sp
jpayne@68 100 \fB\-b\fP <size>
jpayne@68 101 .RS 4
jpayne@68 102 Use a Bloom filter of this size (raw bytes or with K/M/G/T) to
jpayne@68 103 filter out unique k\-mers. This is useful if exact filtering with \fB\-m\fP
jpayne@68 104 uses too much memory. However, some unique k\-mers may pass
jpayne@68 105 erroneously, and copies cannot be counted beyond 2. Implies \fB\-r\fP.
jpayne@68 106 .RE
jpayne@68 107 .sp
jpayne@68 108 \fB\-m\fP <int>
jpayne@68 109 .RS 4
jpayne@68 110 Minimum copies of each k\-mer required to pass noise filter for
jpayne@68 111 reads. Implies \fB\-r\fP. [1]
jpayne@68 112 .RE
jpayne@68 113 .sp
jpayne@68 114 \fB\-c\fP <num>
jpayne@68 115 .RS 4
jpayne@68 116 Target coverage. Sketching will conclude if this coverage is
jpayne@68 117 reached before the end of the input file (estimated by average
jpayne@68 118 k\-mer multiplicity). Implies \fB\-r\fP.
jpayne@68 119 .RE
jpayne@68 120 .sp
jpayne@68 121 \fB\-g\fP <size>
jpayne@68 122 .RS 4
jpayne@68 123 Genome size. If specified, will be used for p\-value calculation
jpayne@68 124 instead of an estimated size from k\-mer content. Implies \fB\-r\fP.
jpayne@68 125 .RE
jpayne@68 126 .SS "Sketching (alphabet)"
jpayne@68 127 .sp
jpayne@68 128 \fB\-n\fP
jpayne@68 129 .RS 4
jpayne@68 130 Preserve strand (by default, strand is ignored by using canonical
jpayne@68 131 DNA k\-mers, which are alphabetical minima of forward\-reverse
jpayne@68 132 pairs). Implied if an alphabet is specified with \fB\-a\fP or \fB\-z\fP.
jpayne@68 133 .RE
jpayne@68 134 .sp
jpayne@68 135 \fB\-a\fP
jpayne@68 136 .RS 4
jpayne@68 137 Use amino acid alphabet (A\-Z, except BJOUXZ). Implies \fB\-n\fP, \fB\-k\fP 9.
jpayne@68 138 .RE
jpayne@68 139 .sp
jpayne@68 140 \fB\-z\fP <text>
jpayne@68 141 .RS 4
jpayne@68 142 Alphabet to base hashes on (case ignored by default; see \fB\-Z\fP).
jpayne@68 143 K\-mers with other characters will be ignored. Implies \fB\-n\fP.
jpayne@68 144 .RE
jpayne@68 145 .sp
jpayne@68 146 \fB\-Z\fP
jpayne@68 147 .RS 4
jpayne@68 148 Preserve case in k\-mers and alphabet (case is ignored by default).
jpayne@68 149 Sequence letters whose case is not in the current alphabet will be
jpayne@68 150 skipped when sketching.
jpayne@68 151 .RE
jpayne@68 152 .SH "SEE ALSO"
jpayne@68 153 .sp
jpayne@68 154 mash(1)