Question: Why map reads back to assembly?
gravatar for macielrodriguez2
11 months ago by
macielrodriguez230 wrote:

Hi! I wanted to know why (and if) is useful to map the reads back to the assembled sequence. Does this gives validation about the coherence of the assembly?

ADD COMMENTlink written 11 months ago by macielrodriguez230

Yes. More specifically you can evaluate the coverage of the assembly to see that you don't have weird things going on.

ADD REPLYlink written 11 months ago by Asaf8.4k

Mapping reads back to the genome is useful to check completeness: you would expect ~99% of reads mapped, depending on your sample. Also, it can be used to detect collapsed regions, usually repetitive DNA, by identifying high coverage regions: for example >3 times the average.

ADD REPLYlink modified 11 months ago • written 11 months ago by alex.zaccaron170
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