Abstract
Ancient DNA is typically highly degraded with appreciable cytosine deamination, and contamination with present-day DNA often complicates the identification of endogenous molecules. Together, these factors impede accurate assembly of the endogenous ancient mitochondrial genome. We present schmutzi, an iterative approach to jointly estimate present-day human contamination in ancient human DNA datasets and reconstruct the endogenous mitochondrial genome. By using sequence deamination patterns and fragment length distributions, schmutzi accurately reconstructs the endogenous mitochondrial genome sequence even when contamination exceeds 50 %. Given sufficient coverage, schmutzi also produces reliable estimates of contamination across a range of contamination rates. Availability: https://bioinf.eva.mpg.de/schmutzi/ license:GPLv3.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-015-0776-0) contains supplementary material, which is available to authorized users.
Highlights
Advances in sequencing and improved methods for the extraction of ancient DNA have enabled the study of ancient genomes
When extracting DNA from ancient human remains, microbial DNA often forms the bulk of all recoverable fragments [3], which, together with contaminating DNA from individuals who handled the ancient sample, is sequenced along with the endogenous DNA [4]
Previous approaches to reconstructing ancient mitochondrial genomes include the mapping iterative assembler (MIA), which iteratively calls a consensus from the DNA fragments [7]
Summary
Advances in sequencing and improved methods for the extraction of ancient DNA (aDNA) have enabled the study of ancient genomes. ADNA molecules, tend to be quite short, typically less than 60 bases in length [1], and carry uracils as a result of cytosine deamination. When extracting DNA from ancient human remains, microbial DNA often forms the bulk of all recoverable fragments [3], which, together with contaminating DNA from individuals who handled the ancient sample, is sequenced along with the endogenous DNA [4]. Because ancient endogenous DNA is more likely to be deaminated than the contaminant DNA from presentday humans [8], some studies have restricted the analyses to fragments carrying deaminated cytosines [9, 10]. Using only deaminated fragments reduces the amount of data available for many ancient samples
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