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Add authenticaiton abstraact
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jfy133 committed Sep 18, 2024
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Expand Up @@ -28,7 +28,10 @@ When exploring composition of metagenomic samples, validation of the detected or

In this case, authentication analysis needs to be performed to demonstrate that the detected organism is truly present in the metagenomic sample and is of endogenous and ancient origin.

In this chapter, we explain how to recognise that a detected organism was mis-identified based on breadth / evenness of coverage, how to validate findings using alignments and assess multiple mapping quality metrics, how to detect modern contaminants via deamination profile, DNA fragmentation and post-mortem damage scores.
In this chapter, we explain how to recognise that a detected organism was mis-identified based on breadth / evenness of coverage, how to validate findings using alignments and assess multiple mapping quality metrics, how to detect modern contaminants via deamination profile, DNA fragmentation and post-mortem damage scores.

We will also introduce metaDMG, a tool currently under development, that enables fast and flexible taxonomic profiling as well as the assessment of post-mortem DNA damage in metagenomic datasets of ancient eukaryotic sequences.
We will learn how to execute metaDMG via the command line and explore some primary statistics using R scripts to evaluate deamination patterns and mean fragment length on a temporal scale.

## [Contamination](contamination.qmd)

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