EAGER: efficient ancient genome reconstruction

By Alexander Peltzer, Günter Jäger, A. Herbig, Alexander Seitz, Christian Kniep, J. Krause, K. Nieselt. Genome Biology, 2016

468 citations recorded by the source corpus.

The automated reconstruction of genome sequences in ancient genome analysis is a multifaceted process. Here we introduce EAGER, a time-efficient pipeline, which greatly simplifies the analysis of large-scale genomic data sets. EAGER provides features to preprocess, map, authenticate, and assess the quality of ancient DNA samples. Additionally, EAGER comprises tools to genotype samples to discover, filter, and analyze variants. EAGER encompasses both state-of-the-art tools for each step as well as new complementary tools tailored for ancient DNA data within a single integrated solution in an easily accessible format.

Subfields: Cultural Studies

View Paper: https://www.semanticscholar.org/paper/377282d70a722139efbc08869c96ced840802a85

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Citations in the corpus

Implications and future prospects for evolutionary analyses of DNA in historical herbarium collections (2018, background): “2014), EAGER (Peltzer et al. 2016), and ATLAS (Link et al.”
Comparative performance of the BGISEQ-500 vs Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing (2017, unknown): “…aDNA, e.g., through exploiting blunt end ligations [12], removing steps associated with DNA loss [13], enzyme choice [14], or even focusing on direct ligation to single-stranded DNA [15], as well as improvement in the informatic tools that are used to process the Fastq data generated [16–19].”
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).”