How can I quantify degradation of DNA present in the sample after sequencing?

Question

[ilykos]

What tools are there to approximately quantify the DNA degradation in sequenced data post-alignment (.bam) or on read level (.fq)?

The goal is not to have an absolute metric of degradation, but to compare and stratify different samples in relation to each other. The less interpretation burden the better.

An example of a tool like this would be mapDamage, and I am looking for other options.

[mark.ziemann]

Are you using Illumina short read sequencing? If you are, I'm not sure you will be able to infer the degree of damage, as short DNA fragments can persist in nature for a long time. You could look into softwares used for ancient DNA analysis.

[ilykos]

Thanks, Mark. Yes, all my data is PE150. At the moment I am looking at the output from pyDamage and mapDamage. The latter manages to distinguish between normal-embedded-old, tumor-embedded-old, normal-embedded-recent, and fresh samples, which is promising.

Could you explain further the connection between persistence of DNA fragments and the ability to evaluate the level of degradation?