jpayne@68: '\" t
jpayne@68: .\"     Title: mash-screen
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\-SCREEN" "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\-screen \- determine whether query sequences are within a larger pool of sequences
jpayne@68: .SH "SYNOPSIS"
jpayne@68: .sp
jpayne@68: \fBmash screen\fP [options] <queries>.msh <pool> [<pool>] ...
jpayne@68: .SH "DESCRIPTION"
jpayne@68: .sp
jpayne@68: Determine how well query sequences are contained within a pool of sequences.
jpayne@68: The queries must be formatted as a single Mash sketch file (.msh), created
jpayne@68: with the \f(CRmash sketch\fP command. The <pool> files can be contigs or reads, in
jpayne@68: fasta or fastq, gzipped or not, and "\-" can be given for <pool> to read from
jpayne@68: standard input. The <pool> sequences are assumed to be nucleotides, and will
jpayne@68: be 6\-frame translated if the <queries> are amino acids. The output fields are
jpayne@68: [identity, shared\-hashes, median\-multiplicity, p\-value, query\-ID, query\-comment],
jpayne@68: where median\-multiplicity is computed for shared hashes, based on the number of
jpayne@68: observations of those hashes within the pool.
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 <int>
jpayne@68: .RS 4
jpayne@68: Parallelism. This many threads will be spawned for processing.
jpayne@68: .RE
jpayne@68: .sp
jpayne@68: \fB\-w\fP
jpayne@68: .RS 4
jpayne@68: Winner\-takes\-all strategy for identity estimates. After counting
jpayne@68: hashes for each query, hashes that appear in multiple queries will
jpayne@68: be removed from all except the one with the best identity (ties
jpayne@68: broken by larger query), and other identities will be reduced. This
jpayne@68: removes output redundancy, providing a rough compositional outline.
jpayne@68: .RE
jpayne@68: .SS "Output"
jpayne@68: .sp
jpayne@68: \fB\-i\fP <num>
jpayne@68: .RS 4
jpayne@68: Minimum identity to report. Inclusive unless set to zero, in which
jpayne@68: case only identities greater than zero (i.e. with at least one
jpayne@68: shared hash) will be reported. Set to \-1 to output everything.
jpayne@68: .RE
jpayne@68: .sp
jpayne@68: \fB\-v\fP <num>
jpayne@68: .RS 4
jpayne@68: Maximum p\-value to report.
jpayne@68: .RE
jpayne@68: .SH "SEE ALSO"
jpayne@68: .sp
jpayne@68: mash(1)