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Extend a read with overhang regions from alignment with a longer read

Hi Biostars,

After aligning a read with a longer read, like aligning a short read scaffold with a long read, I want to extend the short read scaffold with the left and right overhang regions (if they exist) after alignment:

read extension

Any help would be appreciated.

extension mapping
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written by anicet.ebou anicet.ebou

there exist software to do this.

have a look, or search for, "gap-filling" (and even some polishing tools do this)

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written by lieven.sterck lieven.sterck

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