Mercurial > repos > rliterman > csp2
comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/share/man/man1/mash-screen.1 @ 68:5028fdace37b
planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
| author | jpayne |
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| date | Tue, 18 Mar 2025 16:23:26 -0400 |
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| 67:0e9998148a16 | 68:5028fdace37b |
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| 1 '\" t | |
| 2 .\" Title: mash-screen | |
| 3 .\" Author: [see the "AUTHOR(S)" section] | |
| 4 .\" Generator: Asciidoctor 2.0.10 | |
| 5 .\" Date: 2019-12-13 | |
| 6 .\" Manual: \ \& | |
| 7 .\" Source: \ \& | |
| 8 .\" Language: English | |
| 9 .\" | |
| 10 .TH "MASH\-SCREEN" "1" "2019-12-13" "\ \&" "\ \&" | |
| 11 .ie \n(.g .ds Aq \(aq | |
| 12 .el .ds Aq ' | |
| 13 .ss \n[.ss] 0 | |
| 14 .nh | |
| 15 .ad l | |
| 16 .de URL | |
| 17 \fI\\$2\fP <\\$1>\\$3 | |
| 18 .. | |
| 19 .als MTO URL | |
| 20 .if \n[.g] \{\ | |
| 21 . mso www.tmac | |
| 22 . am URL | |
| 23 . ad l | |
| 24 . . | |
| 25 . am MTO | |
| 26 . ad l | |
| 27 . . | |
| 28 . LINKSTYLE blue R < > | |
| 29 .\} | |
| 30 .SH "NAME" | |
| 31 mash\-screen \- determine whether query sequences are within a larger pool of sequences | |
| 32 .SH "SYNOPSIS" | |
| 33 .sp | |
| 34 \fBmash screen\fP [options] <queries>.msh <pool> [<pool>] ... | |
| 35 .SH "DESCRIPTION" | |
| 36 .sp | |
| 37 Determine how well query sequences are contained within a pool of sequences. | |
| 38 The queries must be formatted as a single Mash sketch file (.msh), created | |
| 39 with the \f(CRmash sketch\fP command. The <pool> files can be contigs or reads, in | |
| 40 fasta or fastq, gzipped or not, and "\-" can be given for <pool> to read from | |
| 41 standard input. The <pool> sequences are assumed to be nucleotides, and will | |
| 42 be 6\-frame translated if the <queries> are amino acids. The output fields are | |
| 43 [identity, shared\-hashes, median\-multiplicity, p\-value, query\-ID, query\-comment], | |
| 44 where median\-multiplicity is computed for shared hashes, based on the number of | |
| 45 observations of those hashes within the pool. | |
| 46 .SH "OPTIONS" | |
| 47 .sp | |
| 48 \fB\-h\fP | |
| 49 .RS 4 | |
| 50 Help | |
| 51 .RE | |
| 52 .sp | |
| 53 \fB\-p\fP <int> | |
| 54 .RS 4 | |
| 55 Parallelism. This many threads will be spawned for processing. | |
| 56 .RE | |
| 57 .sp | |
| 58 \fB\-w\fP | |
| 59 .RS 4 | |
| 60 Winner\-takes\-all strategy for identity estimates. After counting | |
| 61 hashes for each query, hashes that appear in multiple queries will | |
| 62 be removed from all except the one with the best identity (ties | |
| 63 broken by larger query), and other identities will be reduced. This | |
| 64 removes output redundancy, providing a rough compositional outline. | |
| 65 .RE | |
| 66 .SS "Output" | |
| 67 .sp | |
| 68 \fB\-i\fP <num> | |
| 69 .RS 4 | |
| 70 Minimum identity to report. Inclusive unless set to zero, in which | |
| 71 case only identities greater than zero (i.e. with at least one | |
| 72 shared hash) will be reported. Set to \-1 to output everything. | |
| 73 .RE | |
| 74 .sp | |
| 75 \fB\-v\fP <num> | |
| 76 .RS 4 | |
| 77 Maximum p\-value to report. | |
| 78 .RE | |
| 79 .SH "SEE ALSO" | |
| 80 .sp | |
| 81 mash(1) |