| Software Resource | Brief Description and Homepage |
|---|---|
| Aladyn | Tools to investigate how demographic parameters, populations genetics and abiotic conditions affect the rate of adaptation http://www.katja-schiffers.eu/research.html |
| ALF | A Simulation Framework for Genome Evolution http://www.cbrg.ethz.ch/alf |
| ART | ART is a set of simulation tools to generate synthetic next-generation sequencing data by mimicking real sequencing process with empirical error models or quality profiles. http://www.niehs.nih.gov/research/resources/software/biostatistics/art/ |
| Bayesian Serial SimCoal | Bayesian Serial SimCoal, (BayeSSC) is a modification of SIMCOAL 1.0, a program written by Laurent Excoffier, John Novembre, and Stefan Schneider. http://www.stanford.edu/group/hadlylab/ssc/index.html |
| BaySICS | An integral platform with a graphical interface for statistical inference based on approximate Bayesian computation. https://sites.google.com/site/baysicsabc/ |
| BEERS | BEERS was designed to benchmark RNA-Seq alignment algorithms and also algorithms that aim to reconstruct different isoforms and alternate splicing from RNA-Seq data http://cbil.upenn.edu/BEERS/ |
| BOTTLENECK | Bottleneck is a program for detecting recent effective population size reductions from allele data frequencies http://www.ensam.inra.fr/URLB/bottleneck/bottleneck.html |
| BottleSim | BottleSim is a computer simulation program for simulating the process of population bottlenecks http://chkuo.name/software/BottleSim.html |
| CASS | Protein Sequence Simulation http://www.wyomingbioinformatics.org/LiberlesGroup/CASS/ |
| CDPOP | CDPOP is a landscape genetics tool for simulating the emergence of spatial genetic structure in populations resulting from specified landscape processes governing organism movement behavior. http://cel.dbs.umt.edu/CDPOP |
| Classical Genetics Simulator | Web-based simulation software http://www.cgslab.com/ |
| CoaSim | CoaSim is a tool for simulating the coalescent process with recombination and geneconversion under various demographic models. http://users-birc.au.dk/mailund/CoaSim/index.html |
| cosi | The cosi package is written in C and is available as a tar file. http://www.broadinstitute.org/~sfs/cosi/ |
| CS-PSeq-Gen | A program to simulate the evolution of protein sequences under the constraints of the information of a particular reconstructed phylogeny http://bioserv.rpbs.univ-paris-diderot.fr/software/CS-PSeq-Gen.html |
| DAWG | An application designed to simulate the evolution of recombinant DNA sequences in continuous time http://scit.us/projects/dawg |
| Easypop | EASYPOP is an individual based model intended to simulate datasets under a very broad range of conditions http://www.unil.ch/dee/page36926_fr.html |
| EggLib | EggLib is a C++/Python library and program package for evolutionary genetics and genomics. http://egglib.sourceforge.net/ |
| EpiSIM | EpiSIM: simulation of multiple epistasis, linkage disequilibrium patterns and haplotype blocks for genome-wide interaction analysis https://sourceforge.net/projects/episimsimulator/files/ |
| EvolSimulator | A simulation test bed for hypotheses of genome evolution http://acb.qfab.org/acb/evolsim/ |
| EvolveAGene | A realistic coding sequence simulation program that separates mutation from selection and allows the user to set selection conditions http://bellinghamresearchinstitute.com/software/index.html |
| fastsimcoal | A continuous-‐time coalescent simulator of genomic diversity under arbitrarily complex evolutionary scenarios http://cmpg.unibe.ch/software/fastsimcoal/ |
| FastSLINK | Simulation of Marker and Phenotype Data in Pedigrees http://watson.hgen.pitt.edu/ |
| FFPopSim | C++/Python library for population genetics. http://webdav.tuebingen.mpg.de/ffpopsim/ |
| FLUX SIMULATOR | The Flux Simulator aims at providing a deterministic in silico reproduction of the experimental pipelines for RNA-Seq, employing a minimal set of parameters. http://flux.sammeth.net/simulator.html |
| forqs | Forward-in-time simulation of Recombination, Quantitative Traits, and Selection https://bitbucket.org/dkessner/forqs |
| ForSim | ForSim: A Forward Evolutionary Computer Simulation http://anth.la.psu.edu/research/weiss-lab/research/research |
| ForwSim | The program given below is based on the algorithm described in Padhukasahasram et al. 2008 to simulate genetic drift in a standard Wright-Fisher process. http://badri-populationgeneticsimulators.blogspot.com/ |
| FPG | Forward Population Genetic simulation https://bio.cst.temple.edu/~hey/software/software.htm#FPG |
| FREGENE | FREGENE is a C++ program that simulates sequence-like data over large genomic regions in large diploid populations. http://www.ebi.ac.uk/projects/BARGEN |
| FIGG | FIGG is a genome simulation tool that uses known or theorized variation frequency, per a given fragment size and grouped by GC content across a genome to model new genomes in FASTA format while tracking applied mutations for use in analysis http://insilicogenome.sourceforge.net/ |
| fwdpp | A C++ template library for implementing efficient forward simulations. http://molpopgen.github.io/fwdpp/ |
| GAMETES | Genetic Architecture Model Emulator for Testing and Evaluating Software: Simulates complex SNP models with pure, strict epistatic interactions with n-loci. http://sourceforge.net/projects/gametes/?source=navbar |
| GASP | Genometric Analysis Simulation Program. A software tool for testing and investigating methods in statistical genetics by generating samples of family data based on user specified models. http://research.nhgri.nih.gov/gasp/ |
| GCTA | Genome-wide Complex Trait Analysis http://www.complextraitgenomics.com/software/gcta/download.html |
| GemSIM | Next generation sequencing read simulator http://sourceforge.net/projects/gemsim/ |
| GeneArtisan | Simulation of Markers in Case-Control Study Designs http://www.rannala.org/?page_id=241 |
| GENOME | A rapid coalescent-based whole genome simulator http://www.sph.umich.edu/csg/liang/genome/ |
| GenomePop2 | GenomePop2 is a specialization of the program GenomePop just to manage SNPs under more flexible and useful settings. If you need models with more than 2 alleles please use the GenomePop program version. http://webs.uvigo.es/acraaj/GenomePop2.htm |
| GenomeSimla | GenomeSIMLA is currently under development- however, we have a beta release that we are asking to be tested http://chgr.mc.vanderbilt.edu/genomeSIMLA/ |
| GENS2 | Simulates interactions among two genetic and one environmental factor and also allows for epistatic interactions. https://sourceforge.net/projects/gensim/ |
| GWAsimulator | A rapid whole genome simulation program http://biostat.mc.vanderbilt.edu/wiki/Main/GWAsimulator |
| HAP-SAMPLE | An association simulator for candidate regions or genome scans http://www.hapsample.org/ |
| HAPGEN | A simulator for the simulation of case control datasets at SNP markers https://mathgen.stats.ox.ac.uk/genetics_software/hapgen/hapgen2.html |
| HapSim | A simulation tool for generating haplotype data with pre-specified allele frequencies and LD coefficients http://cran.r-project.org/web/packages/hapsim/index.html |
| HAPSIMU | A program that simulates heterogeneous populations with various known and controllable structures under the continuous migration model or the discrete model http://l.web.umkc.edu/liujian/ |
| IBDsim | IBDSim is a computer package for the simulation of genotypic data under general isolation by distance models. http://raphael.leblois.free.fr/ |
| indel-Seq-Gen | A biological sequence simulation program that simulates highly divergent DNA sequences and protein superfamilies http://bioinfolab.unl.edu/~cstrope/iSG/ |
| Indelible | A powerful and flexible simulator of biological evolution http://abacus.gene.ucl.ac.uk/software/indelible/ |
| invertFREGENE | InvertFREGENE is a forward-in-time simulator of inversions in population genetic data http://www.ebi.ac.uk/projects/BARGEN/ |
| kernalPop | A spatially explicit population genetic simulation engine http://cran.r-project.org/src/contrib/Archive/kernelPop/ |
| MaCS | Markovian Coalescent Simulator http://www-hsc.usc.edu/~garykche/ |
| Mason | A package for the simulation of nucleotide data. http://www.seqan.de/projects/mason/ |
| mbs | modifying Hudson's ms software to generate samples of DNA sequences with a biallelic site under selection http://www.sendou.soken.ac.jp/esb/innan/InnanLab/software.html |
| Mendel's Accountant | Mendel's Accountant (MENDEL) is an advanced numerical simulation program for modeling genetic change over time and was developed collaboratively by Sanford, Baumgardner, Brewer, Gibson and ReMine http://mendelsaccount.sourceforge.net/ |
| MetaSim | A tool to generate collections of synthetic reads that reflect the diverse taxonomical composition of typical metagenome data sets http://ab.inf.uni-tuebingen.de/software/metasim/ |
| mlcoalsim | Multilocus Coalescent Simulations http://code.google.com/p/mlcoalsim-v1/ |
| ms | The purpose of this program is to allow one to investigate the statistical properties of such samples, to evaluate estimators or statistical tests, and generally to aid in the interpretation of polymorphism data sets. http://home.uchicago.edu/~rhudson1/source/mksamples.html |
| msHOT | The purpose of this program is to allow one to investigate the statistical properties of such samples, to evaluate estimators or statistical tests, and generally to aid in the interpretation of polymorphism data sets. http://home.uchicago.edu/~rhudson1/ |
| msms | A coalescent Simlation tool with selection. http://www.mabs.at/ewing/msms/index.shtml |
| MySSP | A program for the simulation of DNA sequence evolution across a phylogenetic tree http://www.rosenberglab.net/software.php |
| Nemo | A forward-time, individual-based, genetically explicit, and stochastic simulation program designed to study the evolution of genetic markers, life history traits, and phenotypic traits in a flexible (meta-)population framework. http://nemo2.sourceforge.net/ |
| NetRecodon | Coalescent simulation of coding DNA sequences with recombination (inter and intracodon), migration and demography http://code.google.com/p/netrecodon/ |
| PEDAGOG | Software for simulating eco-evolutionary population dynamics https://bcrc.bio.umass.edu/pedigreesoftware/node/5 |
| phenosim | A tool to add phenotypes to simulated genotypes http://evoplant.uni-hohenheim.de/doku.php?id=software:software |
| PhyloSim | An R package for the Monte Carlo simulation of sequence evolution http://www.ebi.ac.uk/goldman-srv/phylosim/ |
| pIRS | Profile-based Illumina pair-end reads simulator https://code.google.com/p/pirs/ |
| ProteinEvolver | Simulation of protein evolution along phylogenies under structure-based substitution models http://code.google.com/p/proteinevolver/ |
| QMSim | QTL and Marker Simulator http://www.aps.uoguelph.ca/~msargol/qmsim/ |
| quantiNEMO | An individual-based program for the analysis of quantitative traits with explicit genetic architecture potentially under selection in a structured population http://www2.unil.ch/popgen/softwares/quantinemo/ |
| RECOAL | Simulates new haplotype data from a reference population of haplotypes. ftp://popgen.usc.edu/ |
| Recodon | Coalescent simulation of coding DNA sequences with recombination, migration and demography http://code.google.com/p/recodon/ |
| rlsim | A package for simulating RNA-seq library preparation with parameter estimation http://bit.ly/rlsim-git |
| Rmetasim | Rmetasim is a front-end for the metasim engine that is implemented as a package that runs in the statistical computing environment R http://cran.r-project.org/web/packages/rmetasim/index.html |
| RNA Seq Simulator | RSS takes SAM alignment files from RNA-Seq data and simulates over dispersed, multiple replica, differential, non-stranded RNA-Seq datasets. http://useq.sourceforge.net/cmdLnMenus.html#RNASeqSimulator |
| Rose | Random model of sequence evolution http://bibiserv.techfak.uni-bielefeld.de/rose/ |
| scrm | A coalescent simulator optimized for long sequences and large samples. https://scrm.github.io/ |
| SelSim | SelSim is a program for Monte Carlo simulation of DNA polymorphism data for a recom- bining region within which a single bi-allelic site has experienced natural selection http://www.well.ox.ac.uk/~spencer/SelSim/ |
| Seq-Gen | An application for the Monte Carlo simulation of molecular sequence evolution along phylogenetic trees. http://tree.bio.ed.ac.uk/software/seqgen/ |
| SEQPower | Statistical power analysis for sequence-based association studies http://bioinformatics.org/spower/ |
| SeqSIMLA | SeqSIMLA can simulate sequence data with user-specified disease and quantitative trait models. Family or unrelated case-control data can be simulated. http://seqsimla.sourceforge.net/ |
| Serial NetEvolve | A flexible utility for generating serially-sampled sequences along a tree or recombinant network http://biorg.cis.fiu.edu/SNE/ |
| SFS_CODE | SFS_CODE can perform forward population genetic simulations under a general Wright-Fisher model with arbitrary migration, demographic, selective, and mutational effects. http://sfscode.sourceforge.net/SFS_CODE/index/index.html |
| SIBSIM | Quantitative phenotype simulation in extended pedigrees http://sourceforge.net/projects/sibsim/ |
| SimAdapt | A spatially explicit, individual-based, forward-time, landscape-genetic simulation model combined with a landscape cellular automaton. http://www.openabm.org/model/3137 |
| SIMCOAL2 | A coalescent program for the simulation of complex recombination patterns over large genomic regions under various demographic models http://cmpg.unibe.ch/software/simcoal2/ |
| SimCopy | An R package simulating the evolution of copy number profiles along a tree. http://bit.ly/simcopy |
| SIMLA | SIMLA is a SIMuLAtion program that generates data sets of families for use in Linkage and Association studies. http://www.chg.duke.edu/research/simla.html |
| SimPed | A Simulation Program to Generate Haplotype and Genotype Data for Pedigree Structures http://bioinformatics.org/simped/ |
| Simprot | A program to simulate protein evolution by substitution, insertion and deletion http://www.uhnresearch.ca/labs/tillier/software.htm#3 |
| SimRare | Rare variant simulation and analysis tool http://code.google.com/p/simrare/ |
| simuGWAS | A forward-time simulator that simulates realistic samples for genome-wide association studies. http://simupop.sourceforge.net/Cookbook/SimuGWAS |
| simuPOP | simuPOP is a general-purpose individual-based forward-time population genetics simulation environment. http://simupop.sourceforge.net/ |
| SISSI | A software tool to generate data of related sequences along a given phylogeny, taking into account user defined system of neighbourhoods and instantaneous rate matrices. http://www.cibiv.at/software/sissi/ |
| SMARTPOP | Simulating Mating Alliance as a Reproductive Tactic for Populations http://smartpop.sourceforge.net/ |
| SNPsim | Coalescent simulation of hotspot recombination http://code.google.com/p/phylosoftware/ |
| SPIP | SPIP simulates the transmission of genes from parents to offspring in a population having demographic structure defined by the user http://swfsc.noaa.gov/textblock.aspx?Division=FED&id=3434 |
| Splatche | Spatial and Temporal Coalescences in Heterogeneous Environment http://www.splatche.com/ |
| srv | Simulator of Rare Varaints (srv) is a simulator for the simulation of the introduction and evolution of (rare) genetic variants. http://simupop.sourceforge.net/Cookbook/SimuRareVariants |
| SUP | SLINK/FastSLINK utility program http://mlemire.freeshell.org/software.html |
| TreesimJ | A flexible, forward-time population genetic simulator http://code.google.com/p/treesimj/ |
| Vortex | VORTEX is an individual-based simulation model for population viability analysis (PVA). http://www.vortex9.org/vortex.html |
| Wessim | Whole Exome Sequencing SIMulator http://sak042.github.io/Wessim/ |
Entering edit mode
10.2 years ago
wangyi2412
▴
250
Hi, everyone!
I am studying the performance of my algorithm, where I need simulation. I looked up the ones used by 1000genomes, but people there said it was outdated, and suggested finding a new one.
I overheard some software called ART, but cannot find it on web.
I also read some similar paper which used simulation, but all of them did not point out what existing software or data sets they used.
Beside the software or datasets to do the simulations in box, I want to know more about the details of and the principle behind the simulation.
The settings are like this:
- First construct the diploid of a human(only consider SNPs/indels, not including other type of variations)
- Generate templates with Gussian distributed length and coming with equal prob from the 4 strand of DNA(+/- strand of two homologous chromosomes, with the error rate similar with that of the sequencing machine like illumina hiseq 2000
- Get 100 bp reads from each template.
The key is how to construct the diploid of a human so that it best resemble a "typical" person in a population in study. Anyone has any idea? Randomly select of a bp to be different from the ref with the prob. of the mutation rate, say 1%? But the mutation rate should be different on different regions, so how to simulate this scenario? Or to the aim of the study, as long as the simulation is not for study depending on the distribution of the variations, this could be omitted?
Thank you very much!
Yi
Whoa! That's one gigantic list! Goes to show the richness in just any subdomain of bioinformatics.
5 years later, this is still a very impressive list. I have nothing to add but a (unfortunately not so recent) paper that might be of use as additional reference
https://dx.doi.org/10.1038%2Fnrg.2016.57
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5224698/
Originally posted by @Joseph Hughes
BBMap's RandomReads: Generates single-ended or paired Illumina reads, or PacBio reads, from a genome. Also has a metagenome mode.