ArticleBMC bioinformatics2014
SInC: an accurate and fast error-model based simulator for SNPs, Indels and CNVs coupled with a read generator for short-read sequence data.
Article in BMC bioinformatics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
- Comparative study of tools for copy number variation detection using next-generation sequencing data.Scientific reports · 2025Article
- A copy number variation detection method based on OCSVM algorithm using multi strategies integration.Scientific reports · 2025Article
- OTSUCNV: an adaptive segmentation and OTSU-based anomaly classification method for CNV detection using NGS data.BMC genomics · 2024Article
- DTDHM: detection of tandem duplications based on hybrid methods using next-generation sequencing data.PeerJ · 2024Article
- satmut_utils: a simulation and variant calling package for multiplexed assays of variant effect.Genome biology · 2023Article
- Boquila: NGS read simulator to eliminate read nucleotide bias in sequence analysis.Turkish journal of biology = Turk biyoloji dergisi · 2023Article
- CNV-PCC: An efficient method for detecting copy number variations from next-generation sequencing data.Frontiers in bioengineering and biotechnology · 2022Article
- svBreak: A New Approach for the Detection of Structural Variant Breakpoints Based on Convolutional Neural Network.BioMed research international · 2022Article
- Identification of Copy Number Alterations from Next-Generation Sequencing Data.Advances in experimental medicine and biology · 2022Article
- EvalDNA: a machine learning-based tool for the comprehensive evaluation of mammalian genome assembly quality.BMC bioinformatics · 2021Article
- Article
- The cp genome characterization of Adenium obesum: Gene content, repeat organization and phylogeny.Saudi journal of biological sciences · 2021Article
- A novel machine learning approach (svmSomatic) to distinguish somatic and germline mutations using next-generation sequencing data.Zoological research · 2021Article
- SomatoSim: precision simulation of somatic single nucleotide variants.BMC bioinformatics · 2021Article
- Phylotranscriptomic analysis ofSaudi journal of biological sciences · 2021Article
- SimuSCoP: reliably simulate Illumina sequencing data based on position and context dependent profiles.BMC bioinformatics · 2020Article
- SCSIM: Jointly simulating correlated single-cell and bulk next-generation DNA sequencing data.BMC bioinformatics · 2020Article
- A broad survey of DNA sequence data simulation tools.Briefings in functional genomics · 2020Review
- DINTD: Detection and Inference of Tandem Duplications From Short Sequencing Reads.Frontiers in genetics · 2020Article
- SECNVs: A Simulator of Copy Number Variants and Whole-Exome Sequences From Reference Genomes.Frontiers in genetics · 2020Article
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4 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundThe rapid advancements in the field of genome sequencing are aiding our understanding on many biological systems. In the last five years, computational biologists and bioinformatics specialists have come up with newer, better and more efficient tools towards the discovery, analysis and interpretation of different genomic variants from high-throughput sequencing data. Availability of reliable simulated dataset is essential and is the first step towards testing any newly developed analytical tools for variant discovery. Although there are tools currently available that can simulate variants, none present the possibility of simulating all the three major types of variations (Single Nucleotide Polymorphisms, Insertions and Deletions and Copy Number Variations) and can generate reads taking a realistic error-model into consideration. Therefore, an efficient simulator and read generator is needed that can simulate variants taking the error rates of true biological samples into consideration.
resultsWe report SInC (Snp, Indel and Cnv) an open-source variant simulator and read generator capable of simulating all the three common types of biological variants taking into account a distribution of base quality score from a most commonly used next-generation sequencing instrument from Illumina. SInC is capable of generating single- and paired-end reads with user-defined insert size and with high efficiency compared to the other existing tools. SInC, due to its multi-threaded capability during read generation, has a low time footprint. SInC is currently optimised to work in limited infrastructure setup and can efficiently exploit the commonly used quad-core desktop architecture to simulate short sequence reads with deep coverage for large genomes.
conclusionsWe have come up with a user-friendly multi-variant simulator and read-generator tools called SInC. SInC can be downloaded from http://sourceforge.net/projects/sincsimulator.
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