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Citations per year

Number of citations per year for the bioinformatics software tool EAGER

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Popular tool citations

chevron_left Read alignment Duplicate read removal Adapter trimming Ancient DNA analysis chevron_right
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EAGER specifications


Unique identifier OMICS_20211
Software type Pipeline/Workflow
Interface Graphical user interface
Restrictions to use Academic or non-commercial use
Input data A reference genome.
Input format FASTA
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
License GNU General Public License version 3.0
Computer skills Medium
Stability Stable
Maintained Yes




No version available



  • person_outline Alexander Peltzer

Additional information

http://eager.readthedocs.io/en/latest/contents/installation.html Tuto: http://eager.readthedocs.io/en/latest/contents/tutorials.html

Publication for EAGER

EAGER citations


Ancient genomes reveal a high diversity of Mycobacterium leprae in medieval Europe

PLoS Pathog
PMCID: 5944922
PMID: 29746563
DOI: 10.1371/journal.ppat.1006997

[…] The data processing after screening for all samples was carried out as previously described [] with modifications of using the EAGER pipeline []. For all samples except the Danish ones the processed reads were mapped to the three M. leprae loci gyrA, proS, and RLEP and characteristic damage profiles were calculated for the M. […]


Ancient DNA study reveals HLA susceptibility locus for leprosy in medieval Europeans

Nat Commun
PMCID: 5931558
PMID: 29717136
DOI: 10.1038/s41467-018-03857-x

[…] sets produced for all ancient samples contained paired-end reads with varying numbers of overlapping nucleotides as well as artificial adapter sequences. We used ClipAndMerge v1.7.3, a module of the EAGER pipeline, to clip adapter sequences, merge corresponding paired-end reads in overlapping regions and to trim the resulting reads. These steps are explained in detail below. We used the default o […]


Inferring genetic origins and phenotypic traits of George Bähr, the architect of the Dresden Frauenkirche

Sci Rep
PMCID: 5794802
PMID: 29391530
DOI: 10.1038/s41598-018-20180-z

[…] General RAW data processing for the initial shallow whole genome sequencing (WGS), mitochondrial capture dataset and the 390 K SNP capture data was done using the EAGER pipeline. In all cases, sequence adapters were clipped with Clip&Merge with default settings and the paired end reads were merged respectively. For the initial WGS and the 390 K SNP capture data […]


The genetic prehistory of the Baltic Sea region

Nat Commun
PMCID: 5789860
PMID: 29382937
DOI: 10.1038/s41467-018-02825-9

[…] equenced on a HiSeq4000 for 75 cycles. Sequencing strategies and facilities are summarized in Supplementary Data , column AE.After demultiplexing, resulting sequence data were further processed using EAGER. This included mapping with BWA (v0.6.1) against UCSC genome browser’s human genome reference GRCh37/hg19, and removing duplicate reads with same orientation and start and end positions. To avoi […]


Central European Woolly Mammoth Population Dynamics: Insights from Late Pleistocene Mitochondrial Genomes

Sci Rep
PMCID: 5735091
PMID: 29255197
DOI: 10.1038/s41598-017-17723-1
call_split See protocol

[…] Endogenous DNA quantification, aDNA authentication and mitochondrial genome reconstruction were performed with an in-house version of the NGS data processing pipeline EAGER v1.92 using a hybrid reference consisting of the African elephant nuclear genome and the woolly mammoth mitochondrial genome (NCBI Accession: GCA_000001905.1 and NC_007596.2 respectively).The fi […]


Deeply divergent archaic mitochondrial genome provides lower time boundary for African gene flow into Neanderthals

Nat Commun
PMCID: 5500885
PMID: 28675384
DOI: 10.1038/ncomms16046
call_split See protocol

[…] Sequenced molecules were converted from bcl to fastq files and reads containing the defining library indexes were binned in an individual folder. The EAGER pipeline was used for all subsequent data processing. Initially adapter and index sequences were trimmed off. Only merged reads where forward and reverse reads overlapped by at least 10 bp were […]

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EAGER institution(s)
Center for Bioinformatics (ZBIT), Integrative Transcriptomics, Eberhard-Karls-Universität, Tübingen, Germany; Institute for Archaeological Sciences, Archaeo- & Palaeogenetics, Tübingen, Germany; Senckenberg Center for Human Evolution and Palaeoenvironment, Tübingen, Germany; QNIB Inc, Böddenstedt, Germany; Max Planck Institute for the Science of the Human History, Jena, Germany
EAGER funding source(s)
Supported by the Max Planck Society.

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