elPrep statistics

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Citations per year

Number of citations per year for the bioinformatics software tool elPrep

Tool usage distribution map

This map represents all the scientific publications referring to elPrep per scientific context
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Associated diseases


Popular tool citations

chevron_left SNP detection SNV detection File indexation File format conversion File merging File filtering File sampling File comparison File intersection File parsing-extraction File splitting File sorting chevron_right
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elPrep specifications


Unique identifier OMICS_32988
Name elPrep
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input format SAM,BAM
Biological technology Illumina
Operating system Unix/Linux
License GNU Affero General Public License version 3
Computer skills Advanced
Version 4.0.1
Stability Stable
Maintained Yes




No version available


  • person_outline Charlotte Herzeel

Publications for elPrep

elPrep citations


Evaluating the necessity of PCR duplicate removal from next generation sequencing data and a comparison of approaches

BMC Bioinformatics
PMCID: 4965708
PMID: 27454357
DOI: 10.1186/s12859-016-1097-3

[…] ates containing an amplification-induced error may cause a variant calling algorithm to misidentify the error as a true variant. Several programs exist to remove or mark PCR duplicates (e.g. SEAL [], elPrep [], FastUniq [], etc.), but in this work we focus on the two most commonly used approaches: Picard MarkDuplicates (http://broadinstitute.github.io/picard/) and SAMTools rmdup [, ].SAMTools and […]


elPrep: High Performance Preparation of Sequence Alignment/Map Files for Variant Calling

PLoS One
PMCID: 4504710
PMID: 26182406
DOI: 10.1371/journal.pone.0132868

[…] elPrep provides the option to process preparation pipelines per genomic region, a practice for splitting up sequencing workloads. However, it is not trivial to apply this technique to the Picard algor […]

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elPrep institution(s)
ExaScience Life Lab, imec, Leuven, Belgium; Department of Information Technology, Ghent University - imec, Ghent, Belgium

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