Wgsim protocols

Wgsim specifications

Information


Unique identifier OMICS_00260
Name Wgsim
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Documentation


Wgsim IN pipelines

 (11)
2018
PMCID: 5831535
PMID: 29490610
DOI: 10.1186/s12859-018-2077-6

[…] the implanted cnvs, there were 20 small cnvs (<1kbs), 86 median-size cnvs (between 1k and 3k bps), and 94 large cnvs (>3kbs). next, we used the artificial chromosome as a template and applied wgsim, a sequencing simulator (part of the samtools) [37], to generate 100bps paired-end reads from the template. a total of 50 million paired-end reads were simulated yielding a sequencing coverage […]

2017
PMCID: 5403047
PMID: 28418314
DOI: 10.3201/eid2305.161165

[…] runs were carried out using the miseq and hiseq technologies, respectively. raw reads were quality checked using fastqc v0.10.1 (22), and primers were trimmed by using cutadapt (23). we used wgsim software (24) to simulate sequence reads for publicly available, complete whole-genome sequences., a detailed description of the bioinformatic analyses is available in the online technical […]

2017
PMCID: 5716257
PMID: 29202713
DOI: 10.1186/s12863-017-0568-5

[…] it has chosen to replace, thereby providing a clear audit trail of the actions taken to create any simulated genomes., next, to simulate ngs data, derived from our simulated hybridized genomes, wgsim [27] was applied against the simulated sequence files, generating 50 million paired-end reads that are 75 bp in length, with end-to-end read sizes of 500 bp. the diploid model of read […]

2017
PMCID: 5716257
PMID: 29202713
DOI: 10.1186/s12863-017-0568-5

[…] against the simulated sequence files, generating 50 million paired-end reads that are 75 bp in length, with end-to-end read sizes of 500 bp. the diploid model of read generation was employed in wgsim and the reads modeled to simulate sequencing errors, indels, and snps using the default configuration parameters., read sets for 3 simulated hybridized genomes were then aligned […]

2016
PMCID: 4869914
PMID: 27185408
DOI: 10.7554/eLife.14552.034

[…] possibility that our mtdna variant analysis has been influenced by numts., we first assessed the potential contribution of numts present within the canfam3.1 assembly to our variant calling. we used wgsim (https://github.com/lh3/wgsim) to simulate sequence reads from canfam3.1 (excluding the mt chromosome) to a coverage of 0.3x (i.e. the average nuclear genome coverage sequenced as part […]

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