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  • Help with demultiplexing inline dual barcodes on paired end Illumina sequences

    If I've missed the obvious tool for this - sorry, I've certainly looked. Have tried FASTX toolbox, Sabre and allprep-py. Everything thus far seems aimed at single barcodes or dual indices.

    We are sequencing amplicons with inline barcodes that reside on each end of the amplicon (= 2 barcodes per amplicon) using Illumina paired-end sequencing. The barcodes are on the 5' end of each of the mate-pair reads.
    All barcode sequences are the same length.
    For example:
    Sample1_R1 = 5' AAAAAA------------------, Sample1_R2 = 5' GGGGGG-------------
    Sample2_R1 = 5' AAAAAA----------------------, Sample2_R2 = 5' TTTTTT-----------------

    Ideally, we'd like to demultiplex with mismatch tolerance (e.g. 1 on each barcode).
    Last edited by Kurt Lamour; 10-05-2015, 11:45 AM. Reason: Clarity

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