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DNemulator specifications

Information


Unique identifier OMICS_09921
Name DNemulator
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Martin Frith

Publication for DNemulator

DNemulator citations

 (4)
library_books

EAGLE: Explicit Alternative Genome Likelihood Evaluator

2018
BMC Med Genomics
PMCID: 5918433
PMID: 29697369
DOI: 10.1186/s12920-018-0342-1

[…] against the human reference genome (hg19) provided by a Sanger sequencing based assessment []. We then simulated paired-end reads of length 100 bp, with insert size 500±30 bp at ∼30× coverage, using DNemulator [].The variants from NS12911 capture the challenge of evaluating putative variants in mutational hotspots and in low complexity and other repetitive regions. Notably, real indels often occu […]

library_books

Detection of differentially methylated regions from bisulfite seq data by hidden Markov models incorporating genome wide methylation level distributions

2015
BMC Genomics
PMCID: 4682380
PMID: 26681544
DOI: 10.1186/1471-2164-16-S12-S3

[…] We simulated bisulfite-converted reads using DNemulator []. The human chromosome × (chrX) was used as a reference. Methylation levels were assigned for all CpG sites in the chrX. 87-bp sinlgle-end reads were generated from random loci in the chr […]

library_books

Jitterbug: somatic and germline transposon insertion detection at single nucleotide resolution

2015
BMC Genomics
PMCID: 4603299
PMID: 26459856
DOI: 10.1186/s12864-015-1975-5

[…] et for each depth-of-coverage thus contains reads which correspond to the homozygous, heterozygous and low-cell-fraction tumor TEI.Reads were simulated from the modified reference sequences using the DNemulator package (www.cbrc.jp/dnemulator/) [] and fastq files from the 1000 Genomes Project sample NA18506 (http://www.ncbi.nlm.nih.gov/sra/ERX009608) as a model for sequencing errors, with fragment […]

library_books

An approximate Bayesian approach for mapping paired end DNA reads to a reference genome

2013
Bioinformatics
PMCID: 3624798
PMID: 23413433
DOI: 10.1093/bioinformatics/btt073

[…] Although it is desirable to work with real datasets, they are accompanied by the problem of not knowing the true genomic location of the reads. This limits us to working with simulated data. Using Dnemulator (www.cbrc.jp/dnemulator), a package for simulating DNA sequencing errors and polymorphisms, we generated paired-end reads from chromosomes 1–22 and X of the human genome hg19. Starting with […]


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DNemulator institution(s)
Computational Biology Research Center, National Institute for Advanced Industrial Science and Technology (AIST), Koto-ku, Tokyo, Japan; Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Japan
DNemulator funding source(s)
Grant-in-Aid for Scientific Research on Innovative Areas 221S0002 from the Ministry of Education, Culture, Sports, Science and Technology in Japan; National Cancer Center Research and Development Fund 23-A-8

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