Open AccessAn efficient pipeline for ancient DNA mapping and recovery of endogenous ancient DNA from whole‐genome sequencing data
Author(s) -
Xu Wenhao,
Lin Yu,
Zhao Keliang,
Li Haimeng,
Tian Yinping,
Ngatia Jacob Njaramba,
Ma Yue,
Sahu Sunil Kumar,
Guo Huabing,
Guo Xiaosen,
Xu Yan Chun,
Liu Huan,
Kristiansen Karsten,
Lan Tianming,
Zhou Xinying
Publication year - 2021
Publication title -
ecology and evolution
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.17
H-Index - 63
ISSN - 2045-7758
DOI - 10.1002/ece3.7056
Subject(s) - ancient dna , dna sequencing , dna , biology , sequencing by hybridization , genome , computational biology , sequencing by ligation , genetics , genomic library , dna sequencer , gene , base sequence , population , demography , sociology
Ancient DNA research has developed rapidly over the past few decades due to improvements in PCR and next‐generation sequencing (NGS) technologies, but challenges still exist. One major challenge in relation to ancient DNA research is to recover genuine endogenous ancient DNA sequences from raw sequencing data. This is often difficult due to degradation of ancient DNA and high levels of contamination, especially homologous contamination that has extremely similar genetic background with that of the real ancient DNA. In this study, we collected whole‐genome sequencing (WGS) data from 6 ancient samples to compare different mapping algorithms. To further explore more effective methods to separate endogenous DNA from homologous contaminations, we attempted to recover reads based on ancient DNA specific characteristics of deamination, depurination, and DNA fragmentation with different parameters. We propose a quick and improved pipeline for separating endogenous ancient DNA while simultaneously decreasing homologous contaminations to very low proportions. Our goal in this research was to develop useful recommendations for ancient DNA mapping and for separation of endogenous DNA to facilitate future studies of ancient DNA.