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Add authenticaiton abstraact
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section-ancient-metagenomics.qmd

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@@ -28,7 +28,10 @@ When exploring composition of metagenomic samples, validation of the detected or
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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.
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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.
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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.
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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.
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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.
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## [Contamination](contamination.qmd)
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