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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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4
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4 <command>usearch
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2
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5 -fastq_mergepairs '$input_forward'
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6 -reverse '$input_reverse'
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7 -fastq_qmaxout $qmaxout
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8 -fastqout '$output'
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9 </command>
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10 <inputs>
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11 <param name='input_forward' type='data' format='fastq,fastqsanger,fastqcssanger' label='The FASTQ filename for the forward reads' />
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12 <param name='input_reverse' type='data' format='fastq,fastqsanger,fastqcssanger' label='The FASTQ filename for the reverse reads' />
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13 <param name='qmaxout' type='integer' value='41' label='Maximum Q score (input files).' />
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14 </inputs>
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15 <outputs>
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16 <data name='output' format='fastq' label="Merge result" />
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17 </outputs>
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18 <tests>
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19 <test>
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20 <param name="input_forward" value="fastq_mergepairs_input1.fq" ftype="fastqsanger" />
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21 <param name="input_reverse" value="fastq_mergepairs_input2.fq" ftype="fastqsanger" />
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22 <param name="qmaxout" value="65" />
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23 <output name="output" file="fastq_mergepairs_output.fq" />
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24 </test>
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25 </tests>
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26 <help>
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27 **What it Does**
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28
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29 Performs merging of paired reads.
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30
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31 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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32
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33 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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34
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35 -----
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36
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37 **Input formats**
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38
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39 Forward read::
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40
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41 @IRIS:7:1:29:952#0/1
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42 TGAGAAGCAAGAAGAAGGTTGGTTAGTGTTTTGGAG
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43 +IRIS:7:1:29:952#0/1
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44 aaabaaaaaaaaaaa`aaY`aa^aaa^a_a_`aa``
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45
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46 Reverse read::
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47
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48 @IRIS:7:1:29:952#0/2
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49 GACTCCAAAACACTAACCAACCTTCTTCTTGCTTCT
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50 +IRIS:7:1:29:952#0/2
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51 aaaabaaaabaaaabbaaaa````__`__^__``__
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52
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53 -----
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54
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55 **Output**
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56
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57 A multiple-fastq file, for example::
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58
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59 @IRIS:7:1:29:952#0/1
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60 TGAGAAGCAAGAAGAAGGTTGGTTAGTGTTTTGGAGTC
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61 +
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62 aaJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJaa
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63
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64 ------
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65
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66 **Author**
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67
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68 Robert C. Edgar (robert@drive5.com)
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69
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70 **Manual**
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71
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72 http://drive5.com/usearch/manual/fastq_mergepairs.html
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73
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74 **Citation**
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75
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76 Please cite one of these papers if you use USEARCH in published work.
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77
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78 Edgar,RC (2010) Search and clustering orders of magnitude faster than BLAST, Bioinformatics 26(19), 2460-2461.
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79 doi: 10.1093/bioinformatics/btq461
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80 </help>
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81 </tool>
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