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E.g. bowhead whale genome has X contigs and Y scaffolds, but couldn't these easily be different numbers?

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    $\begingroup$ Please edit your question to describe a snippet of the whale genomes in question with examples and consider the investigation more carefully. In context the answer is it is of course arbitary. How can it possibly have taxonomic value? $\endgroup$
    – M__
    May 16 '20 at 6:15
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This is purely arbitrary and an artifact of how well the assembly turned out. Better quality assemblies with have fewer and longer contigs.

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  • $\begingroup$ With the ideal for your example being one contig and one scaffold or each chromosome or segment of DNA. $\endgroup$
    – Bioathlete
    May 18 '20 at 17:50

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