IntSIM – An Integrated Simulator of Next-Generation Sequencing Data

IntSIM

:: DESCRIPTION

The IntSim software package has been developed to simulate various genome mutations including germline and somatic variations from next generation sequencing data, and also to generate read data from mixed genomes by considering moderate levels of tumor purity.

::DEVELOPER

IntSIM team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 IntSIM

:: MORE INFORMATION

Citation

IntSIM: An Integrated Simulator of Next-Generation Sequencing Data.
Yuan X, Zhang J, Yang L.
IEEE Trans Biomed Eng. 2016 Apr 29.

SMARTPOP v2.0 – Simulator of Population Genetics and Social Dynamics

SMARTPOP v2.0

:: DESCRIPTION

SMARTPOP (Simulating Mating Alliances as a Reproductive Tactic for Populations) is a fast and flexible forward-in-time simulator for population genetics. Specially developed for speed, it is available in serial and parallel versions. Developed for anthropological inference on human populations, SMARTPOP simulates individuals with sequences of sex-linked DNA (mitochondria, X and Y chromosomes) and autosomes. Studies of social dynamics are enabled using flexible demographic models and social rules of mating.

::DEVELOPER

Professor Murray Cox, Massey University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ windows/MacOsX
  • C++ compiler

:: DOWNLOAD

  SMARTPOP

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2014 Jun 9;15:175. doi: 10.1186/1471-2105-15-175.
SMARTPOP: inferring the impact of social dynamics on genetic diversity through high speed simulations.
Guillot EG, Cox MP1.

MANYCELL 1.0 – Simulator for Cellular Systems

MANYCELL 1.0

:: DESCRIPTION

ManyCell is a multiscale simulator for populations of cells where each cell is described by a full ODE model. It uses COPASI for the molecular level and an agent based simulator for the cell level.

::DEVELOPER

Mendes Research Group

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java
  • Apache Tomcat
  • COPASI

:: DOWNLOAD

 ManyCell

:: MORE INFORMATION

MaCS 0.5d – Markovian Coalescent Simulator

MaCS 0.5d

:: DESCRIPTION

MaCS is a simulator of the coalescent process that simulates geneologies spatially across chromosomes as a Markovian process. The algorithm is similar to the SMC algorithm (McVean and Cardin, Phil Trans Soc R B 2005) in that the algorithm scales linearly in time with respect to sample size and sequence length. However, it more accurately models the true coalescent, while supporting all demographic scenarios found in the popular program MS (Hudson, Bioinformatics 2002) making this program appropriate for simulating data for structured populations in genome wide association studies.

::DEVELOPER

Gary K. Chen, Ph.D.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  MaCS

:: MORE INFORMATION

Citation

Genome Res. 2009 Jan;19(1):136-42. Epub 2008 Nov 24.
Fast and flexible simulation of DNA sequence data.
Chen GK, Marjoram P, Wall JD.

TESD 1.0 – Transposable Element Simulator Dynamics

TESD 1.0

:: DESCRIPTION

TESD simulates the number of genomic TE copies in different populations across generations (according to the Island Model), using classical models of TE dynamics. The parameters of the models (transposition and excision rates, selection intensity, recombination rate, migration rate, population sizes and number of populations) are defined by the users.

::DEVELOPER

TESD team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux /  Mac OsX / Windows
  • Java

:: DOWNLOAD

  TESD

:: MORE INFORMATION

Citation:

Grégory Deceliere, Yann Letrillard, Sandrine Charles and Christian Biémont
TESD: a transposable element dynamics simulation environment
Bioinformatics November 1, 2006 22:2702-2703

NFsim 1.11 – Biochemical Reaction Simulator

NFsim 1.11

:: DESCRIPTION

NFsim (Network Free Stochastic Simuloator) is a free, open-source, biochemical reaction simulator designed to handle systems that have a large or even infinite number of possible molecular interactions or states. NFsim also has advanced and flexible options for simulating coarse-grained representations of complex nonlinear reaction mechanisms.

NFsim is ideal for modeling polymerization, aggregation, and cooperative reactions that cannot be handled with traditional stochastic or ODE simulators. Models are specified in the BioNetGen Langauge, providing a powerful model building environment.

::DEVELOPER

the Emonet lab at Yale University and the Faeder lab at the University of Pittsburgh

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX

:: DOWNLOAD

NFsim

:: MORE INFORMATION

Citation:

Efficient modeling, simulation and coarse-graining of biological complexity with NFsim.
Sneddon MW, Faeder JR, Emonet T.
Nat Methods. 2011 Feb;8(2):177-83. doi: 10.1038/nmeth.1546.

SVEngine – Allele Specific and Haplotype Aware Structural Variants Simulator

SVEngine

:: DESCRIPTION

SVEngine (Structural Variants Engine) is a multi-purpose and self-contained simulator for whole genome scale spike-in of thousands of SV events of various types in both single-sample and matched sample scenarios.

::DEVELOPER

Ji Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Python

:: DOWNLOAD

SVEngine

:: MORE INFORMATION

Citation

Gigascience. 2018 Jul 1;7(7). doi: 10.1093/gigascience/giy081.
SVEngine: an efficient and versatile simulator of genome structural variations with features of cancer clonal evolution.
Xia LC, Ai D, Lee H, Andor N, Li C, Zhang NR, Ji HP

PaSS – A PacBio Sequencing Simulator

PaSS

:: DESCRIPTION

PaSS is a fast sequencing simulator for PacBio sequencing with a high fidelity. It will facilitate the evaluation and development of new analysis tools for the PacBio sequencing data.

::DEVELOPER

Dr. Chaochun Wei

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

PaSS

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2019 Jun 21;20(1):352. doi: 10.1186/s12859-019-2901-7.
PaSS: a sequencing simulator for PacBio sequencing.
Zhang W, Jia B, Wei C

NeSSM / NeSSMt – Next-generation Sequencing Simulator for Metagenomics / Metatranscriptomics

NeSSM / NeSSMt

:: DESCRIPTION

NeSSM is a tool to generate Next-Generation Sequencing (NGS) reads with parameters set by users. The goal of NeSSM is to generate metagenome sequencing reads close to the reality.

NeSSMt is a metatranscriptome simulator. Using a composition table and reference transcripts or genomes (with annotation file)

::DEVELOPER

Dr. Chaochun Wei

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  NeSSM / NeSSMt

:: MORE INFORMATION

Citation:

PLoS One. 2013 Oct 4;8(10):e75448. doi: 10.1371/journal.pone.0075448. eCollection 2013.
NeSSM: a Next-generation Sequencing Simulator for Metagenomics.
Jia B1, Xuan L, Cai K, Hu Z, Ma L, Wei C.

myPresto 5.000 / omegagene 0.38 – Medicinally Yielding PRotein Engineering SimulaTOr

myPresto 5.000 / omegagene 0.38

:: DESCRIPTION

myPresto is a program suite composed of several molecular simulations for drug development.

myPresto/omegagene is a Molecular Dynamics Simulation Engine.

::DEVELOPER

myPresto team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
:: DOWNLOAD

myPresto

:: MORE INFORMATION

Citation

myPresto/omegagene: a GPU-accelerated molecular dynamics simulator tailored for enhanced conformational sampling methods with a non-Ewald electrostatic scheme.
Kasahara K, Ma B, Goto K, Dasgupta B, Higo J, Fukuda I, Mashimo T, Akiyama Y, Nakamura H.
Biophys Physicobiol. 2016 Sep 7;13:209-216.