Ancient dna study: Practical aspects

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.