Identify sample mix from NGS data
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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