Identify sample mix from NGS data


Hi Everyone,

I am constructing a pipeline to profile cell cultures using NGS data.
To validate the purity of a sample, I am now using Centrifuge for taxonomic classification, to screen for cross-contamination.

This approach works well but I would like to include a tool or method that could detect a case where samples are mixed from the same species.

This could be a human cell line that is contaminated by another human cell line.
Fictional example: NA12878 contaminated by HeLa cell line.

In my current approach, I detect my sample as 100% human. But how do I make sure it is not human cells from different cell lines or individuals?

I am fairly new to Cell line authentication so any answers or advice are helpful! 🙂






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