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Wessim specifications

Information


Unique identifier OMICS_00259
Name Wessim
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Publication for Wessim

Wessim citations

 (5)
library_books

Bamgineer: Introduction of simulated allele specific copy number variants into exome and targeted sequence data sets

2018
PLoS Comput Biol
PMCID: 5891060
PMID: 29590101
DOI: 10.1371/journal.pcbi.1006080

[…] to validate specific tools and settings with limited adaptability to other tools. More generalizable approaches aim at the de novo generation of sequencing reads according to a reference genome (e.g. wessim[], Art-illumina[], and dwgsim[]. However, de novo simulated reads do not necessarily capture subtle features of empirical data, such as read coverage distribution, DNA fragment insert size, qua […]

library_books

Comprehensive benchmarking of SNV callers for highly admixed tumor data

2017
PLoS One
PMCID: 5636151
PMID: 29020110
DOI: 10.1371/journal.pone.0186175

[…] For each tumor data set, we used Wessim [] to generate 100 bp Illumina reads with a mean insert size of 300 bp (standard deviation 100) for exome and 200 bp (s.d. 50) for panel data, and median coverage of 70x and 520x for exon and p […]

library_books

ExCNVSS: A Noise Robust Method for Copy Number Variation Detection in Whole Exome Sequencing Data

2017
Biomed Res Int
PMCID: 5494116
PMID: 28698882
DOI: 10.1155/2017/9631282

[…] ome 1 of the 10 HapMap samples, in which the performance of ExCNVSS was compared with those of ExCNVSS_noRatio, ExomeCNV, Contra, and Excavator. Here, ExomeCNV, Contra, and Excavator adopted the same Wessim data set as the control.In general, selecting the optimal parameter matching the characteristics of the data is crucial in increasing an algorithm's performance. However, finding the optimal pa […]

library_books

Detailed simulation of cancer exome sequencing data reveals differences and common limitations of variant callers

2017
BMC Bioinformatics
PMCID: 5209852
PMID: 28049408
DOI: 10.1186/s12859-016-1417-7

[…] was sampled from a Dirichlet distribution with concentration parameter 18 for all clones. We generated 16 DNA sequences by introducing the variants into the hg19 reference DNA sequence and then used Wessim [] to create artificial reads based on an Illumina error model. For more details, see Additional file : Section B. It is important to note that the simulation might influence the extent of cert […]

library_books

Simulating Next Generation Sequencing Datasets from Empirical Mutation and Sequencing Models

2016
PLoS One
PMCID: 5125660
PMID: 27893777
DOI: 10.1371/journal.pone.0167047

[…] Several features of NEAT were inspired by existing tools, but have not been as comprehensively implemented. Wessim’s “probe hybridization” approach is useful for simulating whole exome sequencing, without a current NEAT equivalent. NEAT simply samples reads that cover targeted regions with an increased freq […]

Citations

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Wessim institution(s)
Department of Computer Science and Engineering and Department of Electrical and Computer Engineering, University of California at San Diego, La Jolla, CA, USA

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