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  • Contig and scaffold N50

    Hi all,

    Is it possible for contig and scaffold N50s to be very similar (e.g. within 2-3k bp) or the exact same? I have seen a few examples of this in some de-novo assemblies that I am working with and just want to make sure this is OK.

    Thanks for any thoughts!

  • #2
    PacBio assemblies will have contig and scaffold stats that are very close. I guess single-end Illumina or paired-end Illumina on short fragments would also be like that?
    Providing nextRAD genotyping and PacBio sequencing services. http://snpsaurus.com

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    • #3
      I am using paired end Illumina reads. Usually I see that the contig N50 is 1/2 or 2/3 of scaffold N50, so I was a bit concerned when we got some with exactly the same contig/scaffold N50

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