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DeDup specifications


Unique identifier OMICS_20213
Name DeDup
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Windows
Programming languages Java
License GNU General Public License version 3.0
Computer skills Advanced
Version 0.12.3
Stability Stable
Java Runtime Environment
Maintained Yes




No version available



  • person_outline Alexander Peltzer

DeDup citations


Applications of Bayesian network models in predicting types of hematological malignancies

Sci Rep
PMCID: 5934387
PMID: 29725024
DOI: 10.1038/s41598-018-24758-5

[…] to a few hundred cases, those approaches are not generally suitable to model many (thousands of) genes in a Bayesian network. One workaround is to filter genes before BN learning (e.g.,, and also the dedup function in the bnlearn package), which is inefficient due to information loss. The genes in a gene module are either highly correlated or highly anticorrelated, and they generally contribute to […]


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

[…] mFiles I=$BAMs O=$OUTsamtools index $OUTwhere $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 […]


A survey of functional genomic variation in domesticated chickens

PMCID: 5902831
PMID: 29661130
DOI: 10.1186/s12711-018-0390-1

[…] s sequenced on an Illumina HiSeq machine. We used Sickle software to trim the sequences [], BWA-MEM (version 0.7.15, []) to map the WGS data to the chicken reference genome (Galgal5) [], the Samtools dedup function to discard duplicate reads [], and GATK IndelRealigner to perform local realignments of reads around indels []. […]


Early and late feathering in turkey and chicken: same gene but different mutations

PMCID: 5863816
PMID: 29566646
DOI: 10.1186/s12711-018-0380-3

[…] d paired-end 101 bp reads. We used the Sickle software to trim sequences [], BWA-MEM (version 0.7.15) to map the whole-genome sequencing data to the turkey reference genome (Melgal5) [], the Samtools dedup function to remove duplicate reads [], the GATK IndelRealigner to perform local realignments of reads around indels [] and Qualimap to obtain mapping statistics []. […]


An RNA Seq atlas of gene expression in mouse and rat normal tissues

Sci Data
PMCID: 5726313
PMID: 29231921
DOI: 10.1038/sdata.2017.185
call_split See protocol

[…] --genomeLoad NoSharedMemory Create BAM file index (*.bai) using samtools v0.1.18: samtools index /.fastq.gz.Aligned.sortedByCoord.out.bam Mark Duplicates using BamUtils v1.0.11 ‘dedup’ step: bam dedup --in /.fastq.gz.Aligned.sortedByCoord.out.bam \ --log /.fastq.gz.Aligned.out.dupmark.log \ --out /.fastq.gz.A […]


A time series transcriptome analysis of cassava (Manihot esculenta Crantz) varieties challenged with Ugandan cassava brown streak virus

Sci Rep
PMCID: 5575035
PMID: 28852026
DOI: 10.1038/s41598-017-09617-z

[…] h, taking into account the two allowed mismatches. This was tested and confirmed using randomly selected samples of 37 bp or 88 bp (data not shown). The mapped reads were de-duplicated using Picard’s dedup function, correcting for any amplification bias caused during the PCR used in constructing the sequencing libraries. Mapped reads with gene models on the cassava genome were counted with HTseq_c […]

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