An official website of the United States government
GSR: Simulator - FLUX SIMULATOR
| Attribute | Value |
|---|---|
| Title | FLUX SIMULATOR |
| Short Description | The Flux Simulator aims at providing a deterministic in silico reproduction of the experimental pipelines for RNA-Seq, employing a minimal set of parameters. |
| Long Description | The FluxSimulator is the part of the FLUX project that aims at providing an in silico reproduction of the experimental pipelines for RNA-Seq, adopting a minimal set of parameters. Corresponding models were established after analyzing RNA-Seq experiments from different cell types, sample preparation protocols and sequencing platforms. The first step of the FLUX project is-in fact-a transcriptome simulator. Subsequently, common sources of systematic bias in the abundance and distribution of produced reads are mimicked-whether they incur during library construction, or, in the sequencing process. The FluxSimulator provides a flexible base to design benchmark experiments based on the new sequencing technologies, as for instance abundance predictions of the FluxCapacitor. |
| Version | 1.1 |
| Project Started | 2010 |
| Last Release | 11 years, 7 months ago |
| Homepage | http://confluence.sammeth.net/display/SIM/Home |
| Citations | Griebel T, Zacher B, Ribeca P, Raineri E, Lacroix V, Guigó R, Sammeth M, Modelling and simulating generic RNA-Seq experiments with the flux simulator., Nucleic Acids Res, 11-01-2012 [ Abstract, cited in PMC ] |
| GSR Certification |  ✔ Accessibility |
| Last evaluated | 09-07-2017 (2410 days ago) |
| Attribute Category | Attribute |
|---|---|
| Target | |
| Type of Simulated Data | Genotype at Genetic Markers (After version 1.1), Diploid DNA Sequence (After version 1.1), Haploid DNA Sequence, RNA (Simulating number of rna molecules in a simulated cell type, and location and abundance of rna-seq reads), Sex Chromosomes, Mitochondrial DNA, Protein Sequence, |
| Variations | Biallelic Marker (After version 1.1), Multiallelic Marker (After version 1.1), Single Nucleotide Variation (After version 1.1), Insertion and Deletion (After version 1.1), Alternative Splicing (Produces convoluted read stacks from overlapping regions of alternatively processed transcripts.), Missing Genotypes (After version 1.1), Genotype or Sequencing Error, Other (Variations of rna read abundances introduced by technical processes such as nebulization, hydrolysis, reverse transcription, and pcr), |
| Simulation Method | Forward-time (Different molecule populations are produced generation-by-generation during each step of the library preparation.), Resample Existing Data (Sequencing error models are inferred empirically from read mappings.), Other (Rejection-acception subsampling and metropolis-hastings monte-carlo markov chain.), |
| Input | |
| Data Type | Empirical (Read mappings to generate custom error models of the sequencing process, and empirical size distributions after gel segregation), Other (Input of annotated gene models (required) and the genomic sequence (optional).), |
| File format | Program Specific (Par (parameter file) format with flux simulator specific parameters described by (key,value) pairs), Other (Gtf (gene transfer format), fasta format (genome reference sequence)), |
| Output | |
| Data Type | Genotype or Sequence, Phenotypic Trait (The simulated population of expressed rna sequences is a quantitative trait of the simulated cell.), |
| Sequencing Reads | Other (Chi-square and coefficient of variation for read coverage of each transcript (.pro file). statistics of molecule populations after each step), |
| File Format | Fasta or Fastq, Program Specific (The flux simulator outputs intermediary fragments of simulated library (.lib).), |
| Sample Type | Random or Independent, |
| Phenotype | |
| Trait Type | Quantitative (The phenotype of the cell is reflected by the simulated read abundances of expressed transcripts.), Multiple (Read abundances are gene- and transcript-specific.), |
| Determinants | |
| Evolutionary Features | |
| Demographic | |
| Population Size Changes | |
| Gene Flow | |
| Spatiality | |
| Life Cycle | |
| Mating System | |
| Fecundity | |
| Natural Selection | |
| Determinant | |
| Models | |
| Recombination | |
| Mutation Models | |
| Events Allowed | |
| Other | |
| Interface | Command-line, Graphical User Interface, |
| Development | |
| Tested Platforms | Windows, Mac OS X, Linux and Unix, Solaris, |
| Language | Java, |
| License | BSD, |
| GSR Certification | Accessibility, Documentation, Application, Support, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 5
The following 5 publications are selected examples of applications that used FLUX SIMULATOR.
2018
Zhou J, Ma S, Wang D, Zeng J, Jiang T, FreePSI: an alignment-free approach to estimating exon-inclusion ratios without a reference transcriptome., Nucleic Acids Res, 01-25-2018 [Abstract]
2017
Zhang C, Zhang B, Lin LL, Zhao S, Evaluation and comparison of computational tools for RNA-seq isoform quantification., BMC Genomics, 08-07-2017 [Abstract]
Liu Y, Wu P, Zhou J, Johnson-Pais TL, Lai Z, Chowdhury WH, Rodriguez R, Chen Y, XBSeq2: a fast and accurate quantification of differential expression and differential polyadenylation., BMC Bioinformatics, 10-03-2017 [Abstract]
Liu R, Dickerson J, Strawberry: Fast and accurate genome-guided transcript reconstruction and quantification from RNA-Seq., PLoS Comput Biol, 11-01-2017 [Abstract]
Pai AA, Henriques T, McCue K, Burkholder A, Adelman K, Burge CB, The kinetics of pre-mRNA splicing in the <i>Drosophila</i> genome and the influence of gene architecture., Elife, 12-27-2017 [Abstract]