I am using Galaxy main site to analyse MiSeq data of pooled samples. 
Essentially the run produces 3 fastq files consisting of R1, R2 read files and 
a separate index file. They are in the format below.

R1:                  @M00132:6:000000000-A0JG4:1:1:18014:1842 1:N:0:0
                        Sequence data

R2:                  @M00132:6:000000000-A0JG4:1:1:18014:1842 2:N:0:0
                        Sequence data

Index:              @M00132:6:000000000-A0JG4:1:1:18014:1842 1:N:0:0

 I would like to use Galaxy to demultiplex the samples and then analyse them 
individually.  I have found barcode Splitter (version 1.0.0) on Galaxy however 
this tool requires the index to be found at the beginning of the sequence. 
Therefore I am attempting to add the index sequence onto the end of the 
sequence read data. FASTQ joiner (version 1.0.0) joins fastq files, however the 
fastqs to be joint must be distinguished by a /1 or /2 at end of sequence 
identifiers. Does anyone have any advice or experience of demultiplexing data 
in this format?

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