Abstract
The introduction of next generation sequencing into archaeogenetics transformed the field into a powerhouse of the genetic study of human history. Although the processing of ancient DNA sequencing data follows the same basic principle for that of high-quality modern genomes, there are properties specific to ancient DNA molecules that need to be taken into account during data processing and analysis. In this chapter, I summarize the up-to-date practice of key steps of ancient DNA sequence data, such as the removal of Illumina sequencing adapter, read mapping to the reference genome, tabulation of post-mortem chemical damages, estimation of contamination level, and genotype calling. For each step, I highlight the current practices and the underlying logic for them, as well as directions of future method development.
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Jeong, C. (2021). Ancient DNA Study. In: Shin, D.H., Bianucci, R. (eds) The Handbook of Mummy Studies. Springer, Singapore. https://doi.org/10.1007/978-981-15-3354-9_11
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DOI: https://doi.org/10.1007/978-981-15-3354-9_11
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