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annotate CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/share/man/man1/mash-dist.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-dist
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\-DIST" "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\-dist \- estimate the distance of query sequences to references
jpayne@68 32 .SH "SYNOPSIS"
jpayne@68 33 .sp
jpayne@68 34 \fBmash dist\fP [options] <reference> <query> [<query>] ...
jpayne@68 35 .SH "DESCRIPTION"
jpayne@68 36 .sp
jpayne@68 37 Estimate the distance of each query sequence to the reference. Both the
jpayne@68 38 reference and queries can be fasta or fastq, gzipped or not, or Mash sketch
jpayne@68 39 files (.msh) with matching k\-mer sizes. Query files can also be files of file
jpayne@68 40 names (see \fB\-l\fP). Whole files are compared by default (see \fB\-i\fP). The output
jpayne@68 41 fields are [reference\-ID, query\-ID, distance, p\-value, shared\-hashes].
jpayne@68 42 .SH "OPTIONS"
jpayne@68 43 .sp
jpayne@68 44 \fB\-h\fP
jpayne@68 45 .RS 4
jpayne@68 46 Help
jpayne@68 47 .RE
jpayne@68 48 .sp
jpayne@68 49 \fB\-p\fP <int>
jpayne@68 50 .RS 4
jpayne@68 51 Parallelism. This many threads will be spawned for processing. [1]
jpayne@68 52 .RE
jpayne@68 53 .SS "Input"
jpayne@68 54 .sp
jpayne@68 55 \fB\-l\fP
jpayne@68 56 .RS 4
jpayne@68 57 List input. Each query file contains a list of sequence files, one
jpayne@68 58 per line. The reference file is not affected.
jpayne@68 59 .RE
jpayne@68 60 .SS "Output"
jpayne@68 61 .sp
jpayne@68 62 \fB\-t\fP
jpayne@68 63 .RS 4
jpayne@68 64 Table output (will not report p\-values, but fields will be blank if
jpayne@68 65 they do not meet the p\-value threshold).
jpayne@68 66 .RE
jpayne@68 67 .sp
jpayne@68 68 \fB\-v\fP <num>
jpayne@68 69 .RS 4
jpayne@68 70 Maximum p\-value to report. (0\-1) [1.0]
jpayne@68 71 .RE
jpayne@68 72 .sp
jpayne@68 73 \fB\-d\fP <num>
jpayne@68 74 .RS 4
jpayne@68 75 Maximum distance to report. (0\-1) [1.0]
jpayne@68 76 .RE
jpayne@68 77 .SS "Sketching"
jpayne@68 78 .sp
jpayne@68 79 \fB\-k\fP <int>
jpayne@68 80 .RS 4
jpayne@68 81 K\-mer size. Hashes will be based on strings of this many
jpayne@68 82 nucleotides. Canonical nucleotides are used by default (see
jpayne@68 83 Alphabet options below). (1\-32) [21]
jpayne@68 84 .RE
jpayne@68 85 .sp
jpayne@68 86 \fB\-s\fP <int>
jpayne@68 87 .RS 4
jpayne@68 88 Sketch size. Each sketch will have at most this many non\-redundant
jpayne@68 89 min\-hashes. [1000]
jpayne@68 90 .RE
jpayne@68 91 .sp
jpayne@68 92 \fB\-i\fP
jpayne@68 93 .RS 4
jpayne@68 94 Sketch individual sequences, rather than whole files.
jpayne@68 95 .RE
jpayne@68 96 .sp
jpayne@68 97 \fB\-w\fP <num>
jpayne@68 98 .RS 4
jpayne@68 99 Probability threshold for warning about low k\-mer size. (0\-1) [0.01]
jpayne@68 100 .RE
jpayne@68 101 .sp
jpayne@68 102 \fB\-r\fP
jpayne@68 103 .RS 4
jpayne@68 104 Input is a read set. See Reads options below. Incompatible with \fB\-i\fP.
jpayne@68 105 .RE
jpayne@68 106 .SS "Sketching (reads)"
jpayne@68 107 .sp
jpayne@68 108 \fB\-b\fP <size>
jpayne@68 109 .RS 4
jpayne@68 110 Use a Bloom filter of this size (raw bytes or with K/M/G/T) to
jpayne@68 111 filter out unique k\-mers. This is useful if exact filtering with \fB\-m\fP
jpayne@68 112 uses too much memory. However, some unique k\-mers may pass
jpayne@68 113 erroneously, and copies cannot be counted beyond 2. Implies \fB\-r\fP.
jpayne@68 114 .RE
jpayne@68 115 .sp
jpayne@68 116 \fB\-m\fP <int>
jpayne@68 117 .RS 4
jpayne@68 118 Minimum copies of each k\-mer required to pass noise filter for
jpayne@68 119 reads. Implies \fB\-r\fP. [1]
jpayne@68 120 .RE
jpayne@68 121 .sp
jpayne@68 122 \fB\-c\fP <num>
jpayne@68 123 .RS 4
jpayne@68 124 Target coverage. Sketching will conclude if this coverage is
jpayne@68 125 reached before the end of the input file (estimated by average
jpayne@68 126 k\-mer multiplicity). Implies \fB\-r\fP.
jpayne@68 127 .RE
jpayne@68 128 .sp
jpayne@68 129 \fB\-g\fP <size>
jpayne@68 130 .RS 4
jpayne@68 131 Genome size. If specified, will be used for p\-value calculation
jpayne@68 132 instead of an estimated size from k\-mer content. Implies \fB\-r\fP.
jpayne@68 133 .RE
jpayne@68 134 .SS "Sketching (alphabet)"
jpayne@68 135 .sp
jpayne@68 136 \fB\-n\fP
jpayne@68 137 .RS 4
jpayne@68 138 Preserve strand (by default, strand is ignored by using canonical
jpayne@68 139 DNA k\-mers, which are alphabetical minima of forward\-reverse
jpayne@68 140 pairs). Implied if an alphabet is specified with \fB\-a\fP or \fB\-z\fP.
jpayne@68 141 .RE
jpayne@68 142 .sp
jpayne@68 143 \fB\-a\fP
jpayne@68 144 .RS 4
jpayne@68 145 Use amino acid alphabet (A\-Z, except BJOUXZ). Implies \fB\-n\fP, \fB\-k\fP 9.
jpayne@68 146 .RE
jpayne@68 147 .sp
jpayne@68 148 \fB\-z\fP <text>
jpayne@68 149 .RS 4
jpayne@68 150 Alphabet to base hashes on (case ignored by default; see \fB\-Z\fP).
jpayne@68 151 K\-mers with other characters will be ignored. Implies \fB\-n\fP.
jpayne@68 152 .RE
jpayne@68 153 .sp
jpayne@68 154 \fB\-Z\fP
jpayne@68 155 .RS 4
jpayne@68 156 Preserve case in k\-mers and alphabet (case is ignored by default).
jpayne@68 157 Sequence letters whose case is not in the current alphabet will be
jpayne@68 158 skipped when sketching.
jpayne@68 159 .RE
jpayne@68 160 .SH "SEE ALSO"
jpayne@68 161 .sp
jpayne@68 162 mash(1)