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  • Combining de novo assembly and reference scaffold

    What is the best way to combine de novo and reference-guided assemblies? The scaffold of a closely-related species is available and I would like to use it to improve the de novo assembly I have done.

    Many thanks!

  • #2
    I have started playing with PASA which is the only tool I know of for this task. I'd be curious to hear if there are other options and what others' experiences with PASA have been.

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