ArticleGenome biology2015
Schmutzi: estimation of contamination and endogenous mitochondrial consensus calling for ancient DNA.
Article in Genome biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 260 papers.
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Who cites it
260 citing papers in PubMed, 524 citations in OpenAlex.
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- Ancient DNA reveals elite dynastic rule among Iron Age Eurasian Steppe nomads.Science advances · 2026Article
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- Ground squirrel coprolites preserve complex archives of ancient environmental DNA over 700,000 years.Nature communications · 2026Article
- Bioarchaeological analysis illustrates the life of a 16th-century Sámi individual from Kitka, Kuusamo, northern Finland.BMC genomics · 2026Article
- Multiple Genetic Shifts at the Crossroads of the Eastern Steppe and Loess Plateau Over 4,000 Years.Nature communications · 2026Article
- ChASM: a statistically rigorous method for the detection of chromosomal aneuploidies in ancient DNA studies.Bioinformatics (Oxford, England) · 2026Article
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- On the Edge of Empire: Paleogenomic Insights into Roman Dacia.bioRxiv : the preprint server for biology · 2026Article
- An ancient genome of Streptococcus pyogenes from a pre-Columbian Bolivian mummy.Nature communications · 2026Article
- The Genomic Legacy of the Norman Conquest in Rural England.bioRxiv : the preprint server for biology · 2026Article
- Ancient genomes reveal an extensive kinship network and endogamy in a Three-Kingdoms period society in Korea.Science advances · 2026Article
- Genetic genealogy of the Piast dynasty and related European royal families.Nature communications · 2026Article
200 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
unlabelledAncient 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.
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