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Thread Tools |
11-12-2019, 12:33 PM
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#1 |
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Junior Member
Location: USA Join Date: Nov 2019
Posts: 2
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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! 
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11-12-2019, 04:51 PM
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#2 |
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Registered Vendor
Location: Eugene, OR Join Date: May 2013
Posts: 523
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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?
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11-13-2019, 05:19 AM
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#3 |
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Junior Member
Location: USA Join Date: Nov 2019
Posts: 2
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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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| Tags |
| assembly, contigs, n50, scaffolds |
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