ArticleBMC bioinformatics2015
SCNVSim: somatic copy number variation and structure variation simulator.
Article in BMC bioinformatics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- MosaicSim: A Novel Mosaic Variant Simulator Reveals Diminishing Returns of Ultra-High Coverage for Mosaic Variant Detection.bioRxiv : the preprint server for biology · 2025Article
- SISTEM: simulation of tumor evolution, metastasis, and DNA-seq data under genotype-driven selection.Bioinformatics (Oxford, England) · 2025Article
- MOV&RSim: computational modelling of cancer-specific variants and sequencing reads characteristics for realistic tumoral sample simulation.BMC bioinformatics · 2025Article
- SoMaCX: a complex generative genome modeling framework.BMC genomics · 2025Article
- Article
- Assessing the merits: an opinion on the effectiveness of simulation techniques in tumor subclonal reconstruction.Bioinformatics advances · 2024Article
- Boquila: NGS read simulator to eliminate read nucleotide bias in sequence analysis.Turkish journal of biology = Turk biyoloji dergisi · 2023Article
- J-SPACE: a Julia package for the simulation of spatial models of cancer evolution and of sequencing experiments.BMC bioinformatics · 2022Article
- Identification of Copy Number Alterations from Next-Generation Sequencing Data.Advances in experimental medicine and biology · 2022Article
- A benchmark of structural variation detection by long reads through a realistic simulated model.Genome biology · 2021Article
- AmpliconReconstructor integrates NGS and optical mapping to resolve the complex structures of focal amplifications.Nature communications · 2020Article
- SimuSCoP: reliably simulate Illumina sequencing data based on position and context dependent profiles.BMC bioinformatics · 2020Article
- SECNVs: A Simulator of Copy Number Variants and Whole-Exome Sequences From Reference Genomes.Frontiers in genetics · 2020Article
- Next-generation forward genetic screens: using simulated data to improve the design of mapping-by-sequencing experiments in Arabidopsis.Nucleic acids research · 2019Article
- Comprehensive evaluation and characterisation of short read general-purpose structural variant calling software.Nature communications · 2019Article
- SVEngine: an efficient and versatile simulator of genome structural variations with features of cancer clonal evolution.GigaScience · 2018Article
- Pysim-sv: a package for simulating structural variation data with GC-biases.BMC bioinformatics · 2017Article
- Global analysis of somatic structural genomic alterations and their impact on gene expression in diverse human cancers.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- cnvCurator: an interactive visualization and editing tool for somatic copy number variations.BMC bioinformatics · 2015Article
Corrections and comments
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Authors and funding
12 authors.
Funding
Abstract
backgroundSomatically acquired structure variations (SVs) and copy number variations (CNVs) can induce genetic changes that are directly related to tumor genesis. Somatic SV/CNV detection using next-generation sequencing (NGS) data still faces major challenges introduced by tumor sample characteristics, such as ploidy, heterogeneity, and purity. A simulated cancer genome with known SVs and CNVs can serve as a benchmark for evaluating the performance of existing somatic SV/CNV detection tools and developing new methods.
resultsSCNVSim is a tool for simulating somatic CNVs and structure variations SVs. Other than multiple types of SV and CNV events, the tool is capable of simulating important features related to tumor samples including aneuploidy, heterogeneity and purity.
conclusionsSCNVSim generates the genomes of a cancer cell population with detailed information of copy number status, loss of heterozygosity (LOH), and event break points, which is essential for developing and evaluating somatic CNV and SV detection methods in cancer genomics studies.
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