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

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author jpayne
date Tue, 18 Mar 2025 16:23:26 -0400
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jpayne@68 1 '\" t
jpayne@68 2 .\" Title: mash-triangle
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\-TRIANGLE" "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\-triangle \- estimate a lower\-triangular distance matrix
jpayne@68 32 .SH "SYNOPSIS"
jpayne@68 33 .sp
jpayne@68 34 \fBmash triangle\fP [options] <seq1> [<seq2>] ...
jpayne@68 35 .SH "DESCRIPTION"
jpayne@68 36 .sp
jpayne@68 37 Estimate the distance of each input sequence to every other input
jpayne@68 38 sequence. Outputs a lower\-triangular distance matrix in relaxed Phylip
jpayne@68 39 format. The input sequences can be fasta or fastq, gzipped or not, or
jpayne@68 40 Mash sketch files (.msh) with matching k\-mer sizes. Input files can also
jpayne@68 41 be files of file names (see \-l). If more than one input file is provided,
jpayne@68 42 whole files are compared by default (see \-i).
jpayne@68 43 .SH "OPTIONS"
jpayne@68 44 .sp
jpayne@68 45 \fB\-h\fP
jpayne@68 46 .RS 4
jpayne@68 47 Help
jpayne@68 48 .RE
jpayne@68 49 .sp
jpayne@68 50 \fB\-p\fP <int>
jpayne@68 51 .RS 4
jpayne@68 52 Parallelism. This many threads will be spawned for processing. [1]
jpayne@68 53 .RE
jpayne@68 54 .SS "Input"
jpayne@68 55 .sp
jpayne@68 56 \fB\-l\fP
jpayne@68 57 .RS 4
jpayne@68 58 List input. Each query file contains a list of sequence files, one
jpayne@68 59 per line. The reference file is not affected.
jpayne@68 60 .RE
jpayne@68 61 .SS "Output"
jpayne@68 62 .sp
jpayne@68 63 \fB\-C\fP
jpayne@68 64 .RS 4
jpayne@68 65 Use comment fields for sequence names instead of IDs.
jpayne@68 66 .RE
jpayne@68 67 .sp
jpayne@68 68 \fB\-E\fP
jpayne@68 69 .RS 4
jpayne@68 70 Output edge list instead of Phylip matrix, with fields [seq1, seq2,
jpayne@68 71 dist, p\-val, shared\-hashes].
jpayne@68 72 .RE
jpayne@68 73 .sp
jpayne@68 74 \fB\-v\fP <num>
jpayne@68 75 .RS 4
jpayne@68 76 Maximum p\-value to report in edge list. Implies \-E. (0\-1) [1.0]
jpayne@68 77 .RE
jpayne@68 78 .sp
jpayne@68 79 \fB\-d\fP <num>
jpayne@68 80 .RS 4
jpayne@68 81 Maximum distance to report in edge list. Implies \-E. (0\-1) [1.0]
jpayne@68 82 .RE
jpayne@68 83 .SS "Sketching"
jpayne@68 84 .sp
jpayne@68 85 \fB\-k\fP <int>
jpayne@68 86 .RS 4
jpayne@68 87 K\-mer size. Hashes will be based on strings of this many
jpayne@68 88 nucleotides. Canonical nucleotides are used by default (see
jpayne@68 89 Alphabet options below). (1\-32) [21]
jpayne@68 90 .RE
jpayne@68 91 .sp
jpayne@68 92 \fB\-s\fP <int>
jpayne@68 93 .RS 4
jpayne@68 94 Sketch size. Each sketch will have at most this many non\-redundant
jpayne@68 95 min\-hashes. [1000]
jpayne@68 96 .RE
jpayne@68 97 .sp
jpayne@68 98 \fB\-i\fP
jpayne@68 99 .RS 4
jpayne@68 100 Sketch individual sequences, rather than whole files, e.g. for
jpayne@68 101 multi\-fastas of single\-chromosome genomes or pair\-wise gene comparisons.
jpayne@68 102 .RE
jpayne@68 103 .sp
jpayne@68 104 \fB\-w\fP <num>
jpayne@68 105 .RS 4
jpayne@68 106 Probability threshold for warning about low k\-mer size. (0\-1) [0.01]
jpayne@68 107 .RE
jpayne@68 108 .sp
jpayne@68 109 \fB\-r\fP
jpayne@68 110 .RS 4
jpayne@68 111 Input is a read set. See Reads options below. Incompatible with \fB\-i\fP.
jpayne@68 112 .RE
jpayne@68 113 .SS "Sketching (reads)"
jpayne@68 114 .sp
jpayne@68 115 \fB\-b\fP <size>
jpayne@68 116 .RS 4
jpayne@68 117 Use a Bloom filter of this size (raw bytes or with K/M/G/T) to
jpayne@68 118 filter out unique k\-mers. This is useful if exact filtering with \fB\-m\fP
jpayne@68 119 uses too much memory. However, some unique k\-mers may pass
jpayne@68 120 erroneously, and copies cannot be counted beyond 2. Implies \fB\-r\fP.
jpayne@68 121 .RE
jpayne@68 122 .sp
jpayne@68 123 \fB\-m\fP <int>
jpayne@68 124 .RS 4
jpayne@68 125 Minimum copies of each k\-mer required to pass noise filter for
jpayne@68 126 reads. Implies \fB\-r\fP. [1]
jpayne@68 127 .RE
jpayne@68 128 .sp
jpayne@68 129 \fB\-c\fP <num>
jpayne@68 130 .RS 4
jpayne@68 131 Target coverage. Sketching will conclude if this coverage is
jpayne@68 132 reached before the end of the input file (estimated by average
jpayne@68 133 k\-mer multiplicity). Implies \fB\-r\fP.
jpayne@68 134 .RE
jpayne@68 135 .sp
jpayne@68 136 \fB\-g\fP <size>
jpayne@68 137 .RS 4
jpayne@68 138 Genome size. If specified, will be used for p\-value calculation
jpayne@68 139 instead of an estimated size from k\-mer content. Implies \fB\-r\fP.
jpayne@68 140 .RE
jpayne@68 141 .SS "Sketching (alphabet)"
jpayne@68 142 .sp
jpayne@68 143 \fB\-n\fP
jpayne@68 144 .RS 4
jpayne@68 145 Preserve strand (by default, strand is ignored by using canonical
jpayne@68 146 DNA k\-mers, which are alphabetical minima of forward\-reverse
jpayne@68 147 pairs). Implied if an alphabet is specified with \fB\-a\fP or \fB\-z\fP.
jpayne@68 148 .RE
jpayne@68 149 .sp
jpayne@68 150 \fB\-a\fP
jpayne@68 151 .RS 4
jpayne@68 152 Use amino acid alphabet (A\-Z, except BJOUXZ). Implies \fB\-n\fP, \fB\-k\fP 9.
jpayne@68 153 .RE
jpayne@68 154 .sp
jpayne@68 155 \fB\-z\fP <text>
jpayne@68 156 .RS 4
jpayne@68 157 Alphabet to base hashes on (case ignored by default; see \fB\-Z\fP).
jpayne@68 158 K\-mers with other characters will be ignored. Implies \fB\-n\fP.
jpayne@68 159 .RE
jpayne@68 160 .sp
jpayne@68 161 \fB\-Z\fP
jpayne@68 162 .RS 4
jpayne@68 163 Preserve case in k\-mers and alphabet (case is ignored by default).
jpayne@68 164 Sequence letters whose case is not in the current alphabet will be
jpayne@68 165 skipped when sketching.
jpayne@68 166 .RE
jpayne@68 167 .SH "SEE ALSO"
jpayne@68 168 .sp
jpayne@68 169 mash(1)