title: Schmutzi: estimation of contamination and endogenous mitochondrial consensus calling for ancient DNA.
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.
  
  
  BACKGROUND
  https://bioinf.eva.mpg.de/schmutzi/ license:GPLv3.
authors.affiliation: Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig, Germany. gabriel.reno@gmail.com.
authors.forename: Gabriel
authors.initials: G
authors.lastname: Renaud
authors.affiliation: Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig, Germany. viviane_slon@eva.mpg.de.
authors.forename: Viviane
authors.initials: V
authors.lastname: Slon
authors.affiliation: McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, 1280 Main St West, Hamilton, ON, L8S 4L9, Canada. duggana@mcmaster.ca.
authors.forename: Ana T
authors.initials: AT
authors.lastname: Duggan
authors.affiliation: Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig, Germany. janet_kelso@eva.mpg.de.
authors.forename: Janet
authors.initials: J
authors.lastname: Kelso
mesh_terms: D000818:Animals; D001483:Base Sequence; D016384:Consensus Sequence; D059018:DNA Contamination; D004272:DNA, Mitochondrial / Q000737:chemistry*; D054629:Genome, Mitochondrial; D006801:Humans; D059125:Neanderthals / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
chemical_list: D004272:DNA, Mitochondrial