Wgsim protocols

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Wgsim statistics

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Wgsim specifications


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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Wgsim in pipelines

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) [], to generate 100bps paired-end reads from the template. a total of 50 million paired-end reads were simulated yielding a sequencing coverage […]

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

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

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 […]

PMCID: 4939949
PMID: 27400380
DOI: 10.1371/journal.pcbi.1004991

[…] prevalent in marine environments [] (). according to their natural compositions, each genome was in silico sequenced with different coverage (min coverage 1.25x, max coverage 10x, mean coverage 4x). wgsim (version 0.3.0) was used for in silico sequencing to generate pair-end reads with error rate 0.01 and expected read length 100; and the number of reads to be generated were calculated using […]

PMCID: 5112629
PMID: 27852226
DOI: 10.1186/s12864-016-3286-x

[…] ”—v --s 51 --e 71 --i 4 --t 1 --o “-ins_length 250 -min_contig_lgth 500”. the resulting assembly was used to simulate 28x coverage of a long mate-pair library with insert 3000 +/- 270 bp using wgsim (https://github.com/lh3/wgsim) with options “-e 0 -1 100 -2 100 -r 0 -r 0 -x 0 ”. 25x of the simulated long-mate pair data was then coassembled with 125x coverage of the original qc filtered […]

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Wgsim in publications

PMCID: 5904416
PMID: 29666288
DOI: 10.1128/mBio.00575-18

[…] of 2.75, we calculated our statistical power to be greater than 0.8., simulated mapping analysis and mapping statistics. (a and b) one million single-end simulated reads were generated through wgsim from either the entire metatranscriptome (a) or a subset of genes with ec annotations (b). mapping was performed using bowtie 2 with parameters used in the study to the entire transcriptome […]

PMCID: 5895191
PMID: 29732264
DOI: 10.1002/aps3.1034

[…] referenced against the ncbi taxonomy (downloaded august 2016; federhen, ) to identify the lowest common ancestor associated for each classified read., metagenome simulation data were generated using wgsim ( https://github.com/lh3/wgsim) to generate 100,000 reads using the default settings of 70‐bp read‐length average and a base mutation rate of 0.001 and a read error rate of 0. soil metagenome […]

PMCID: 5900883
PMID: 29327410
DOI: 10.1111/1462-2920.14043

[…] libraries: (i) filtered illumina reads were assembled using velvet (version 1.1.04) (zerbino and birney, ), (ii) 1–3 kb simulated paired end reads were created from velvet contigs using wgsim (https://github.com/ih3/wgsim), (iii) illumina reads were assembled with simulated read pairs using allpaths–lg (version r41043) (gnerre et al., ). the 454 titanium standard data and the 454 […]

PMCID: 5843745
PMID: 29519829
DOI: 10.1128/genomeA.00112-18

[…] library was constructed and sequenced using the illumina hiseq 2000 platform, which generated 10,961,766 reads totaling 1,655.2 mb. the filtered illumina reads were assembled using the velvet (), wgsim (https://github.com/lh3/wgsim), and allpaths-lg () tools. the final draft assembly contains 42 contigs in 36 scaffolds, totaling 4.2 mb, with an input read coverage of 268.9-fold. the largest […]

PMCID: 5830760
PMID: 29515871
DOI: 10.1098/rsos.171589

[…] ncbi accession: gcf_000002035.6) digested with the enzyme sbfi. only the primary assembly on 25 chromosomes of grcz11 were retained for in silico digest. by using ‘ezmsim', a modified version of ‘wgsim' [] from rainbow, pe reads of length 125 bp were simulated from a range of insert size libraries initiated from 200 bp and elongation of 10 steps, with each step extends 50 bp. mean depth […]

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