Improving ancient DNA read mapping against modern reference genomes.

BMC Genomics
Mikkel SchubertLudovic Orlando

Abstract

Next-Generation Sequencing has revolutionized our approach to ancient DNA (aDNA) research, by providing complete genomic sequences of ancient individuals and extinct species. However, the recovery of genetic material from long-dead organisms is still complicated by a number of issues, including post-mortem DNA damage and high levels of environmental contamination. Together with error profiles specific to the type of sequencing platforms used, these specificities could limit our ability to map sequencing reads against modern reference genomes and therefore limit our ability to identify endogenous ancient reads, reducing the efficiency of shotgun sequencing aDNA. In this study, we compare different computational methods for improving the accuracy and sensitivity of aDNA sequence identification, based on shotgun sequencing reads recovered from Pleistocene horse extracts using Illumina GAIIx and Helicos Heliscope platforms. We show that the performance of the Burrows Wheeler Aligner (BWA), that has been developed for mapping of undamaged sequencing reads using platforms with low rates of indel-types of sequencing errors, can be employed at acceptable run-times by modifying default parameters in a platform-specific manner. We also e...Continue Reading

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Citations

Nov 10, 2013·Nature Communications·Hucai ZhangMichael Hofreiter
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Datasets Mentioned

BETA
SRP005902
SRA0458620

Methods Mentioned

BETA
Illumina sequencing
Helicos
deamination
PCR
deaminations
Helicos sequencing

Software Mentioned

EquCab2
mapDamage
Helicos true Single Molecule DNA Sequencing platform tSMS )
ANFO
MIA
Helicos tSMS
BWA
Helicos
BWA aligner
Picard

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