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

By Gabriel Renaud, V. Slon, Ana T. Duggan, Janet Kelso. Genome Biology, 2015

454 citations recorded by the source corpus.

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.

Subfields: Archeology, Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/197f45538d3c6df0c9b24a98404589d834f4c0e2

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In Genetics

1. J. Krause

In Molecular Biology

1. J. Krause
2. Alexander Seitz
3. K. Nieselt
4. A. Herbig
5. Christian Kniep
6. Günter Jäger
7. Alexander Peltzer

Citations in the corpus

• EAGER: efficient ancient genome reconstruction (2016, methodology): “Furthermore, contamination estimation and subsequent consensus sequence generation in FastA format can be done within the pipeline using schmutzi [15].”
• From the field to the laboratory: Controlling DNA contamination in human ancient DNA research in the high-throughput sequencing era (2017, unknown): “…patterns are used to assess the authenticity of aDNA, and have been implemented in several recent bioinformatics programs (Helgason et al. 2007; Jónsson et al. 2013; Korneliussen, Albrechtsen, and Nielsen 2014; Skoglund et al. 2014; Renaud et al. 2015; Peltzer et al. 2016; Ginolhac et al. 2011).”