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2
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1 <tool id="usearch_fastq_mergepairs" name="usearch fastq_mergepairs" version="0.0.1">
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2 <description>merging of paired reads</description>
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3 <version_command>usearch -version</version_command>
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12
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4 <command interpreter='bash'>usearch_wrapper.sh
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5 usearch
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6 -fastq_minovlen 0
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7 -quiet
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7
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8 -fastq_mergepairs '$input_forward'
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9 -reverse '$input_reverse'
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11
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10 #if $minovlen != '0':
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7
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11 -fastq_minovlen $minovlen
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12 #end if
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13 -fastq_qmax $qmax
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14 -fastqout '$output'
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2
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15 </command>
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16 <inputs>
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7
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17 <param name="input_forward" type="data" format="fastq,fastqsanger,fastqcssanger" label="File with forward reads" />
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18 <param name="input_reverse" type="data" format="fastq,fastqsanger,fastqcssanger" label="File with reverse reads" />
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11
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19 <param name="minovlen" type="integer" value="0" label="Minimum length of the overlap" help="'0' means no minimum." />
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10
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20 <param name="qmax" type="integer" value="41" label="Maximum Q score for input files" />
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2
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21 </inputs>
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22 <outputs>
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23 <data name='output' format='fastq' label="Merge result" />
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24 </outputs>
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25 <tests>
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26 <test>
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27 <param name="input_forward" value="fastq_mergepairs_input1.fq" ftype="fastqsanger" />
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28 <param name="input_reverse" value="fastq_mergepairs_input2.fq" ftype="fastqsanger" />
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5
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29 <param name="qmax" value="65" />
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2
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30 <output name="output" file="fastq_mergepairs_output.fq" />
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31 </test>
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32 </tests>
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33 <help>
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34 **What it Does**
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35
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36 Performs merging of paired reads.
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37
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38 The FASTQ filename for the forward reads is specified by the -fastq_mergepairs option, and the reverse read filename is specified by the -reverse option. Output files are specified by -fastqout (for FASTQ) and / or -fastaout (for FASTA).
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39
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40 Forward and reverse must be in 1:1 correspondence and must appear in the same order in both files. The labels for the forward and reverse read in a given pair must be identical except for a single position where a '1' appears in the forward read label and a '2' appears in the reverse read label.
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41
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42 -----
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43
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44 **Input formats**
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45
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46 Forward read::
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47
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48 @IRIS:7:1:29:952#0/1
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49 TGAGAAGCAAGAAGAAGGTTGGTTAGTGTTTTGGAG
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50 +IRIS:7:1:29:952#0/1
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51 aaabaaaaaaaaaaa`aaY`aa^aaa^a_a_`aa``
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52
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53 Reverse read::
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54
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55 @IRIS:7:1:29:952#0/2
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56 GACTCCAAAACACTAACCAACCTTCTTCTTGCTTCT
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57 +IRIS:7:1:29:952#0/2
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58 aaaabaaaabaaaabbaaaa````__`__^__``__
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59
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60 -----
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61
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62 **Output**
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63
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64 A multiple-fastq file, for example::
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65
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66 @IRIS:7:1:29:952#0/1
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67 TGAGAAGCAAGAAGAAGGTTGGTTAGTGTTTTGGAGTC
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68 +
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69 aaJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJaa
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70
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71 ------
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72
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73 **Author**
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74
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75 Robert C. Edgar (robert@drive5.com)
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76
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77 **Manual**
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78
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79 http://drive5.com/usearch/manual/fastq_mergepairs.html
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80
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81 **Citation**
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82
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83 Please cite one of these papers if you use USEARCH in published work.
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84
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85 Edgar,RC (2010) Search and clustering orders of magnitude faster than BLAST, Bioinformatics 26(19), 2460-2461.
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86 doi: 10.1093/bioinformatics/btq461
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87 </help>
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88 </tool>
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