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  • Miseq v2 PE library length for Allpaths-LG

    Hello,

    I'd like to use ALLPATHS-LG for de novo assembling of a fungal genome
    (~20 Mbp). I will use Miseq data for the assembling.

    I am wondering the length of fragment for paired read can be longer for the version2 of Miseq.

    In the FAQ of Allpaths-LG, there is a sentence "For longer reads, somewhat longer fragments could be used".

    ###################################
    Q: Do I need paired reads from an “overlapping” fragment library?
    Yes. We use paired reads of length ~100 bases from fragments of size ~180 bp. For longer reads, somewhat longer fragments could be used.
    ###################################

    Now the read length of the Miseq v2 is 250 bp, paired reads from fragments of more than size ~400 bp would be overlapping and can be input for ALLPATHS-LG, right?
    Has anyone try to input overlapping fragment library from the fragments of
    more than 400 bp?

    Many thanks,

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