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Genome Biol. 2015 Oct 12;16:224. doi: 10.1186/s13059-015-0776-0.

Schmutzi: estimation of contamination and endogenous mitochondrial consensus calling for ancient DNA.

Author information

1
Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig, Germany. gabriel.reno@gmail.com.
2
Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig, Germany. viviane_slon@eva.mpg.de.
3
McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, 1280 Main St West, Hamilton, ON, L8S 4L9, Canada. duggana@mcmaster.ca.
4
Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig, Germany. janet_kelso@eva.mpg.de.

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.

PMID:
26458810
PMCID:
PMC4601135
DOI:
10.1186/s13059-015-0776-0
[Indexed for MEDLINE]
Free PMC Article

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