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