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454Scaffolds = 454LargeContigs?

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  • 454Scaffolds = 454LargeContigs?

    I thought the new "scaffold" option in Newbler might do something interesting with my shotgun data even though I thought this term was previously only discussed in relation to paired-end data. Anyway, I have tried doing a de novo assembly of shotgun data both with and without the scaffold option selected. It seems that the scaffold output is identical to the largest contigs (of course there is variation depending upon scaffold and large contig length cutoffs). Is this normal or should I have expected anything different?

  • #2
    The -scaffold option is not intended for assemblies where no paired end data are included. If you do see scaffolds, these are indeed contigs of at least 2 kbp.

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