jpayne@68: '\" t jpayne@68: .\" Title: mash-dist jpayne@68: .\" Author: [see the "AUTHOR(S)" section] jpayne@68: .\" Generator: Asciidoctor 2.0.10 jpayne@68: .\" Date: 2019-12-13 jpayne@68: .\" Manual: \ \& jpayne@68: .\" Source: \ \& jpayne@68: .\" Language: English jpayne@68: .\" jpayne@68: .TH "MASH\-DIST" "1" "2019-12-13" "\ \&" "\ \&" jpayne@68: .ie \n(.g .ds Aq \(aq jpayne@68: .el .ds Aq ' jpayne@68: .ss \n[.ss] 0 jpayne@68: .nh jpayne@68: .ad l jpayne@68: .de URL jpayne@68: \fI\\$2\fP <\\$1>\\$3 jpayne@68: .. jpayne@68: .als MTO URL jpayne@68: .if \n[.g] \{\ jpayne@68: . mso www.tmac jpayne@68: . am URL jpayne@68: . ad l jpayne@68: . . jpayne@68: . am MTO jpayne@68: . ad l jpayne@68: . . jpayne@68: . LINKSTYLE blue R < > jpayne@68: .\} jpayne@68: .SH "NAME" jpayne@68: mash\-dist \- estimate the distance of query sequences to references jpayne@68: .SH "SYNOPSIS" jpayne@68: .sp jpayne@68: \fBmash dist\fP [options] [] ... jpayne@68: .SH "DESCRIPTION" jpayne@68: .sp jpayne@68: Estimate the distance of each query sequence to the reference. Both the jpayne@68: reference and queries can be fasta or fastq, gzipped or not, or Mash sketch jpayne@68: files (.msh) with matching k\-mer sizes. Query files can also be files of file jpayne@68: names (see \fB\-l\fP). Whole files are compared by default (see \fB\-i\fP). The output jpayne@68: fields are [reference\-ID, query\-ID, distance, p\-value, shared\-hashes]. jpayne@68: .SH "OPTIONS" jpayne@68: .sp jpayne@68: \fB\-h\fP jpayne@68: .RS 4 jpayne@68: Help jpayne@68: .RE jpayne@68: .sp jpayne@68: \fB\-p\fP jpayne@68: .RS 4 jpayne@68: Parallelism. This many threads will be spawned for processing. [1] jpayne@68: .RE jpayne@68: .SS "Input" jpayne@68: .sp jpayne@68: \fB\-l\fP jpayne@68: .RS 4 jpayne@68: List input. Each query file contains a list of sequence files, one jpayne@68: per line. The reference file is not affected. jpayne@68: .RE jpayne@68: .SS "Output" jpayne@68: .sp jpayne@68: \fB\-t\fP jpayne@68: .RS 4 jpayne@68: Table output (will not report p\-values, but fields will be blank if jpayne@68: they do not meet the p\-value threshold). jpayne@68: .RE jpayne@68: .sp jpayne@68: \fB\-v\fP jpayne@68: .RS 4 jpayne@68: Maximum p\-value to report. (0\-1) [1.0] jpayne@68: .RE jpayne@68: .sp jpayne@68: \fB\-d\fP jpayne@68: .RS 4 jpayne@68: Maximum distance to report. (0\-1) [1.0] jpayne@68: .RE jpayne@68: .SS "Sketching" jpayne@68: .sp jpayne@68: \fB\-k\fP jpayne@68: .RS 4 jpayne@68: K\-mer size. Hashes will be based on strings of this many jpayne@68: nucleotides. Canonical nucleotides are used by default (see jpayne@68: Alphabet options below). (1\-32) [21] jpayne@68: .RE jpayne@68: .sp jpayne@68: \fB\-s\fP jpayne@68: .RS 4 jpayne@68: Sketch size. Each sketch will have at most this many non\-redundant jpayne@68: min\-hashes. [1000] jpayne@68: .RE jpayne@68: .sp jpayne@68: \fB\-i\fP jpayne@68: .RS 4 jpayne@68: Sketch individual sequences, rather than whole files. jpayne@68: .RE jpayne@68: .sp jpayne@68: \fB\-w\fP jpayne@68: .RS 4 jpayne@68: Probability threshold for warning about low k\-mer size. (0\-1) [0.01] jpayne@68: .RE jpayne@68: .sp jpayne@68: \fB\-r\fP jpayne@68: .RS 4 jpayne@68: Input is a read set. See Reads options below. Incompatible with \fB\-i\fP. jpayne@68: .RE jpayne@68: .SS "Sketching (reads)" jpayne@68: .sp jpayne@68: \fB\-b\fP jpayne@68: .RS 4 jpayne@68: Use a Bloom filter of this size (raw bytes or with K/M/G/T) to jpayne@68: filter out unique k\-mers. This is useful if exact filtering with \fB\-m\fP jpayne@68: uses too much memory. However, some unique k\-mers may pass jpayne@68: erroneously, and copies cannot be counted beyond 2. Implies \fB\-r\fP. jpayne@68: .RE jpayne@68: .sp jpayne@68: \fB\-m\fP jpayne@68: .RS 4 jpayne@68: Minimum copies of each k\-mer required to pass noise filter for jpayne@68: reads. Implies \fB\-r\fP. [1] jpayne@68: .RE jpayne@68: .sp jpayne@68: \fB\-c\fP jpayne@68: .RS 4 jpayne@68: Target coverage. Sketching will conclude if this coverage is jpayne@68: reached before the end of the input file (estimated by average jpayne@68: k\-mer multiplicity). Implies \fB\-r\fP. jpayne@68: .RE jpayne@68: .sp jpayne@68: \fB\-g\fP jpayne@68: .RS 4 jpayne@68: Genome size. If specified, will be used for p\-value calculation jpayne@68: instead of an estimated size from k\-mer content. Implies \fB\-r\fP. jpayne@68: .RE jpayne@68: .SS "Sketching (alphabet)" jpayne@68: .sp jpayne@68: \fB\-n\fP jpayne@68: .RS 4 jpayne@68: Preserve strand (by default, strand is ignored by using canonical jpayne@68: DNA k\-mers, which are alphabetical minima of forward\-reverse jpayne@68: pairs). Implied if an alphabet is specified with \fB\-a\fP or \fB\-z\fP. jpayne@68: .RE jpayne@68: .sp jpayne@68: \fB\-a\fP jpayne@68: .RS 4 jpayne@68: Use amino acid alphabet (A\-Z, except BJOUXZ). Implies \fB\-n\fP, \fB\-k\fP 9. jpayne@68: .RE jpayne@68: .sp jpayne@68: \fB\-z\fP jpayne@68: .RS 4 jpayne@68: Alphabet to base hashes on (case ignored by default; see \fB\-Z\fP). jpayne@68: K\-mers with other characters will be ignored. Implies \fB\-n\fP. jpayne@68: .RE jpayne@68: .sp jpayne@68: \fB\-Z\fP jpayne@68: .RS 4 jpayne@68: Preserve case in k\-mers and alphabet (case is ignored by default). jpayne@68: Sequence letters whose case is not in the current alphabet will be jpayne@68: skipped when sketching. jpayne@68: .RE jpayne@68: .SH "SEE ALSO" jpayne@68: .sp jpayne@68: mash(1)