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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



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  • 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 in publications

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

[…] ], except for the danish samples, which were directly shotgun sequenced. between 406,241 and 12,227,587 short reads were mapped to the m. leprae tn reference genome (refseq id nc_002677.1) using the eager pipeline [] and all samples with at least 7x-fold mean coverage were selected for further analysis (tables , ). for the resulting 10 samples, we used the genome analysis toolkit (gatk) […]

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

[…] $out, where $bams is a string containing all individual-specific bam files to be concatenated, separated by whitespace, and $out is the concatenated bam file., we used dedup v0.9.9, part of the eager pipeline, to identify and remove all duplicate reads in the individual-specific bam files with the default options and the following command:, java -jar dedup.jar -i $in -o $out, where $in […]

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

[…] 101$$\end{document}2×101 cycles., 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 […]

PMCID: 5500885
PMID: 28675384
DOI: 10.1038/ncomms16046

[…] ilan gronau, adam powell, wolfgang haak, maria spyrou and alvise barbieri. we thank frido welker and matthew collins for zooms analyses, alexander peltzer and gabriel renaud for support in running eager and schmutzi, respectively, mannis van oven for access to the updated version of the rnrs reference and annette günzel for graphical support. c.p. and j.k. were supported by the baden […]

PMCID: 5459999
PMID: 28556824
DOI: 10.1038/ncomms15694

[…] hiseq 2500 platform by 2 × 100+7+7 cycles following the manufacturer's protocols for multiplex sequencing (truseq pe cluster kit v3-cbot-hs)., the resulting fastq files have been processed using eager v1.92 (ref. ). to achieve improved coverages at both ends of the mitochondrial reference, we used the circularmapper option in eager. all reads with a mapping quality of at least 30 were kept […]

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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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