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

Question

[anicet.ebou]

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:

Any help would be appreciated.

[lieven.sterck]

there exist software to do this.

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

[anicet.ebou]

Thanks for the tip!