An efficient pipeline for ancient DNA mapping and recovery of endogenous ancient DNA from whole-genome sequencing data
Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › fagfællebedømt
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An efficient pipeline for ancient DNA mapping and recovery of endogenous ancient DNA from whole-genome sequencing data. / 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.
I: Ecology and Evolution, Bind 11, Nr. 1, 2021, s. 390-401.Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › fagfællebedømt
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TY - JOUR
T1 - An efficient pipeline for ancient DNA mapping and recovery of endogenous ancient DNA from whole-genome sequencing data
AU - Xu, Wenhao
AU - Lin, Yu
AU - Zhao, Keliang
AU - Li, Haimeng
AU - Tian, Yinping
AU - Ngatia, Jacob Njaramba
AU - Ma, Yue
AU - Sahu, Sunil Kumar
AU - Guo, Huabing
AU - Guo, Xiaosen
AU - Xu, Yan Chun
AU - Liu, Huan
AU - Kristiansen, Karsten
AU - Lan, Tianming
AU - Zhou, Xinying
PY - 2021
Y1 - 2021
N2 - 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.
AB - 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.
KW - ancient DNA
KW - BWA mem
KW - deamination
KW - DNA damage
KW - genome mapping
U2 - 10.1002/ece3.7056
DO - 10.1002/ece3.7056
M3 - Journal article
C2 - 33437437
AN - SCOPUS:85097820406
VL - 11
SP - 390
EP - 401
JO - Ecology and Evolution
JF - Ecology and Evolution
SN - 2045-7758
IS - 1
ER -
ID: 254667478