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DeDup specifications

Information


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
Requirements
Java Runtime Environment
Maintained Yes

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  • person_outline Alexander Peltzer <>

DeDup in publications

 (11)
PMCID: 5934387
PMID: 29725024
DOI: 10.1038/s41598-018-24758-5

[…] 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 […]

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

[…] i=$bams o=$out, samtools index $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 […]

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

[…] 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 []., we performed population-based variant calling using freebayes software […]

PMCID: 5795009
PMID: 29391547
DOI: 10.1038/s41598-018-20346-9

[…] were trimmed to have an average error rate <1%, no bases with a quality of <q30 and no ambiguities. reads <50 nt in length were discarded; duplicate reads were removed using the program dedup (within geneious) and host contaminating human genome sequences were filtered out using the hg38 database. filtered reads were assembled de novo using stringent assembly conditions: minimum 50 […]

PMCID: 5726313
PMID: 29231921
DOI: 10.1038/sdata.2017.185

[…] , create bam file index (*.bai) using samtools v0.1.18:, samtools index <sample_id>/<sample_id>.fastq.gz.aligned.sortedbycoord.out.bam , mark duplicates using bamutils v1.0.11 ‘dedup’ step:, bam dedup --in <sample_id>/<sample_id>.fastq.gz.aligned.sortedbycoord.out.bam \ , --log <sample_id>/<sample_id>.fastq.gz.aligned.out.dupmark.log \ , --out […]


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