Why map reads back to assembly?
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4.3 years ago

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?

assembly sequence next-gen alignment Assembly • 1.8k views
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Yes. More specifically you can evaluate the coverage of the assembly to see that you don't have weird things going on.

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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.

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