Renaud Gabriel, Slon Viviane, Duggan Ana T, Kelso Janet
Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig, Germany.
McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, 1280 Main St West, Hamilton, ON, L8S 4L9, Canada.
Genome Biol. 2015 Oct 12;16:224. doi: 10.1186/s13059-015-0776-0.
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.
https://bioinf.eva.mpg.de/schmutzi/ license:GPLv3.
古代DNA通常高度降解，存在明显的胞嘧啶脱氨现象，而现代DNA的污染常常使内源性分子的鉴定变得复杂。这些因素共同阻碍了古代内源性线粒体基因组的准确组装。我们提出了schmutzi，这是一种迭代方法，用于联合估计古代人类DNA数据集中的现代人类污染情况，并重建内源性线粒体基因组。通过使用序列脱氨模式和片段长度分布，即使污染超过50%，schmutzi也能准确重建内源性线粒体基因组序列。在有足够覆盖度的情况下，schmutzi还能对一系列污染率下的污染情况做出可靠估计。
https://bioinf.eva.mpg.de/schmutzi/ 许可证：GPLv3
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