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DWGSIM specifications

Information


Unique identifier OMICS_00249
Name DWGSIM
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C, Perl, Python
License GNU General Public License version 2.0
Computer skills Advanced
Version 0.1.12
Stability Stable
Maintained No

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Publication for DWGSIM

DWGSIM in pipelines

 (3)
2018
PMCID: 5945760
PMID: 29478186
DOI: 10.1007/s00122-018-3077-7

[…] or gain of each chromosome of nipponbare or 93-11 in turn (successively). the simulated files were exported as fasta files. next, the 48 simulated fasta files were randomly broken into reads using dwgsim (http://davetang.org/wiki/tiki-index.php?page=dwgsim). in this manner, the simulated fasta datasets were generated with the same criteria as the actual sequencing data except […]

2016
PMCID: 4779607
PMID: 26782936
DOI: 10.1093/gbe/evv263

[…] genome resequencing project v2 (sgrp2) (). where only finished genome sequences were available in public databases (ncbi), the corresponding error-free illumina reads were simulated using dwgsim (http://sourceforge.net/apps/mediawiki/dnaa/)., reads for each isolate were mapped to s. cerevisiae reference genome (ucsc version saccer3) using smalt v0.7.5 aligner […]

2014
PMCID: 4289236
PMID: 25407810
DOI: 10.1186/1471-2164-15-991

[…] to avoid repetitive mapping., the genomic data of publicly available m. tuberculosis strains (format fasta) were included in the analysis through conversion to fastq format reads using the program dwgsim v.0.1.10, and mapped and analyzed as described above. when necessary, dna sequence alignment was performed using the clc sequence viewer v7.6.1 (clc bio®, aarhus n, denmark) and visualized […]


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DWGSIM in publications

 (16)
PMCID: 5846869
PMID: 29568413
DOI: 10.1007/s13258-017-0621-9

[…] the location from which the reads were generated, insert the variants with the desired variant allele frequency, and determine the target region to be sequenced for panel sequencing. therefore, dwgsim (http://github.com/nh13/dwgsim) was only used to report the read generated position and fastq datasets with variants were produced according to the following methods., the reference genome […]

PMCID: 5338827
PMID: 28212378
DOI: 10.1371/journal.pgen.1006630

[…] from both mitochondria and chloroplast genomes are integrated in nuclear genomes. to completely eliminate these regions from our data, sequencing reads were simulated from organelle genome using the dwgsim program (version 0.1.10) and the .fasta files were mapped against the corresponding reference genome. a total of 816,300 bp and 1,697,400 bp were masked in a. thaliana and o. sativa, […]

PMCID: 5125660
PMID: 27893777
DOI: 10.1371/journal.pone.0167047

[…] be more flexible and user-friendly than many others in the field (). the list of existing simulators compared against are those most often used, according to number of paper citations: art, curesim, dwgsim [], gemsim (including the the targeted sequencing functionality of wessim []), mason [], pirs, and sinc []. varsim [] is not explicitly listed as it is a wrapper around dwgsim and art., […]

PMCID: 5048557
PMID: 27716037
DOI: 10.1186/s12859-016-1279-z

[…] interrogated by any of the four agilent sureselectxt human all exon kits (all exon 50mbp, all exon v4, all exon v4 + utrs, and all exon v5 + utrs, http://www.agilent.com)., simulation was done using dwgsim v0.1.11 (https://github.com/nh13/dwgsim/wiki) at six mutation rates (0.05, 0.01, 0.5, 1, 5 and 10 %). illumina paired 100-base reads were simulated to an average per-base coverage of 100x, […]

PMCID: 5010666
PMID: 27590916
DOI: 10.1186/s12864-016-3045-z

[…] of the regions included in the simulation. we compiled 10,768 non-overlapping exonic regions of chromosome 6, from which 100-base paired-end reads were simulated to an average coverage of 100x using dwgsim (additional file : method 1). to investigate the impact of coverage depth on variant calling, we randomly sampled six subsets with coverage depth of 80x, 60x, 40x, 20x, 10x and 5x, […]


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DWGSIM institution(s)
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Beijing Institute of Genomics, Chinese Academy of Science, Beijing, China; Department of Computer Science, University of California Los Angeles, Los Angeles, CA, USA; Department of Biology, Boston College, Chestnut Hill, MA, USA; Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA; 1000 Genome Project Data Processing Subgroup
DWGSIM funding source(s)
Supported by Wellcome Trust/077192/Z/05/Z and NIH Hapmap/1000 Genomes Project grant (U54HG002750).

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