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Add abstract part one
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jfy133 committed Sep 17, 2024
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Expand Up @@ -20,10 +20,15 @@ In this chapter, we will show you how to prepare your sequencing data and subseq

## [Authentication](authentication.qmd)

When exploring composition of metagenomic samples, validation of the detected organisms represents a particular challenge, because it may happen that the detected organism may have have the following characteristics

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1. Was mis-identified (the DNA belongs to another organism than initially thought)
2. Has a modern origin (for example, lab or sequencing contaminant)
3. Is of exogenous origin (for example, an ancient microbe that entered the host post-mortem).

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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.

## [Contamination](contamination.qmd)

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