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  • Newbler Scafolding

    Hi All

    I tried running the newbler 2.6. But when i use the flag -scaffold I don't get any of the three scaffold file. Can some body tell me is it possible to make scaffolds using the single end 454 reads if not then how I can annotate those contigs. Is the blast only solution.

    Regards
    Last edited by figo1019; 02-21-2013, 06:53 AM.

  • #2
    The name of the '-scaffold' flag is misleading. Newbler will never scaffold without mate pairs ('paired end reads', in 454 language). But that's the point: with only single-end reads, all you can make is contigs (by definition, some would say). What '-scaffold'- does is change some aspect of scaffolding (filling gaps with repeat consensus sequences).

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