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  • velveth assembly with single and paired ends

    I have been running some velveth assemblies but not very sure if i have been doing the right thing. Consider the following reads,
    pair two
    >@SLXA-EAS1_89:1:1:672:654/2
    ATTAACAACAAAGGGTAAAAGGCATCATGGCTTCA
    >@SLXA-EAS1_89:1:1:657:649/2
    TGATGCGACGACGCACCTCGTTGTTACGCACTTCA
    >@SLXA-EAS1_89:1:1:708:653/2
    CTGTGGATAACATGGTGTAAGATCCTGTTTATTTT
    >@SLXA-EAS1_89:1:1:675:644/2
    TACTTTTATATGCAAGACCAAATTTACCGATACTT

    pair one
    >@SLXA-EAS1_89:1:1:672:654/1
    GCTACGGAATAAAACCAGGAACAACAGACCCAGCA
    >@SLXA-EAS1_89:1:1:657:649/1
    GCAGAAAATGGGAGTGAAAATCTCCGATGAGCAGC
    >@SLXA-EAS1_89:1:1:708:653/1
    GAGAGAGCAGTGGGCGAGGTTGGGACATGTCATGA
    >@SLXA-EAS1_89:1:1:675:644/1
    GAACATTTATTATAATCCTATTCAATTATAATAAT

    After cleaning, you end up with:
    pair two2
    >@SLXA-EAS1_89:1:1:672:654/2
    ATTAACAACAAAGGGTAAAAGGCATCATGGCTTCA
    >@SLXA-EAS1_89:1:1:657:649/2
    TGATGCGACGACGCACCTCGTTGTTACGCACTTCA
    pair one1
    >@SLXA-EAS1_89:1:1:672:654/1
    GCTACGGAATAAAACCAGGAACAACAGACCCAGCA
    >@SLXA-EAS1_89:1:1:657:649/1
    GCAGAAAATGGGAGTGAAAATCTCCGATGAGCAGC
    and a file of singletons like
    >@SLXA-EAS1_89:1:1:708:653/1
    GAGAGAGCAGTGGGCGAGGTTGGGACATGTCATGA
    >@SLXA-EAS1_89:1:1:675:644/2
    TACTTTTATATGCAAGACCAAATTTACCGATACTT

    I wish to find out if you supply the singleton file to velveth as it is or do you have to reverse compliment all reverse pairs in the singleton file. Has velveth got a way of determining the orientations of the reads using the /1 & /2 tags?

    Please advice.

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