title: EAGER: efficient ancient genome reconstruction.
abstract: BACKGROUND
  The automated reconstruction of genome sequences in ancient genome analysis is a multifaceted process.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Center for Bioinformatics (ZBIT), Integrative Transcriptomics, Eberhard-Karls-Universität, Sand 14, Tübingen, 72076, Germany. alexander.peltzer@uni-tuebingen.de.|Institute for Archaeological Sciences, Archaeo- & Palaeogenetics, Rümelinstraße 23, Tübingen, 72074, Germany. alexander.peltzer@uni-tuebingen.de.|Max Planck Institute for the Science of the Human History, Kahlaische Straße 10, Jena, 07745, Germany. alexander.peltzer@uni-tuebingen.de.
authors.forename: Alexander
authors.initials: A
authors.lastname: Peltzer
authors.affiliation: Center for Bioinformatics (ZBIT), Integrative Transcriptomics, Eberhard-Karls-Universität, Sand 14, Tübingen, 72076, Germany.
authors.forename: Günter
authors.initials: G
authors.lastname: Jäger
authors.affiliation: Center for Bioinformatics (ZBIT), Integrative Transcriptomics, Eberhard-Karls-Universität, Sand 14, Tübingen, 72076, Germany.|Institute for Archaeological Sciences, Archaeo- & Palaeogenetics, Rümelinstraße 23, Tübingen, 72074, Germany.|Max Planck Institute for the Science of the Human History, Kahlaische Straße 10, Jena, 07745, Germany.
authors.forename: Alexander
authors.initials: A
authors.lastname: Herbig
authors.affiliation: Center for Bioinformatics (ZBIT), Integrative Transcriptomics, Eberhard-Karls-Universität, Sand 14, Tübingen, 72076, Germany.
authors.forename: Alexander
authors.initials: A
authors.lastname: Seitz
authors.affiliation: QNIB Inc, Ortfeld 1, Böddenstedt, 29556, Germany.
authors.forename: Christian
authors.initials: C
authors.lastname: Kniep
authors.affiliation: Institute for Archaeological Sciences, Archaeo- & Palaeogenetics, Rümelinstraße 23, Tübingen, 72074, Germany.|Senckenberg Center for Human Evolution and Palaeoenvironment, Rümelinstraße 23, Tübingen, 72074, Germany.|Max Planck Institute for the Science of the Human History, Kahlaische Straße 10, Jena, 07745, Germany.
authors.forename: Johannes
authors.initials: J
authors.lastname: Krause
authors.affiliation: Center for Bioinformatics (ZBIT), Integrative Transcriptomics, Eberhard-Karls-Universität, Sand 14, Tübingen, 72076, Germany.
authors.forename: Kay
authors.identifier: http://orcid.org/0000-0002-1283-7065
authors.initials: K
authors.lastname: Nieselt
mesh_terms: D002874:Chromosome Mapping / Q000379:methods; D005580:Fossils; D016678:Genome; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D057188:Workflow
keywords: Authentication; Bioinformatics; Genome reconstruction; aDNA; aDNA analysis