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Read simulation software tools | Whole-genome sequencing data analysis

In the past few years, high-throughput next-generation sequencing technologies have effectively replaced earlier data types for genome-wide studies measuring gene expression changes and discovering genomic/epigenetic variations, and many tools were…
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SimSeq
Desktop

SimSeq

An illumina paired-end and mate-pair short read simulator. This project…

An illumina paired-end and mate-pair short read simulator. This project attempts to model as many of the quirks that exist in Illumina data as possible. Some of these quirks include the potential for…

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Simulome
Desktop

Simulome

Creates prokaryotic pseudo-genomes. Simulome provides options that can be used…

Creates prokaryotic pseudo-genomes. Simulome provides options that can be used in combination to create mutated variants of the simulated genome, which allows for controlled testing of specific…

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ART
Desktop

ART

A set of simulation tools to generate synthetic next-generation sequencing…

A set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles…

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LongISLND
Desktop

LongISLND In silico Sequencing of Lengthy and Noisy Datatypes

Profiles the characteristics of third generation, single-molecule sequencing…

Profiles the characteristics of third generation, single-molecule sequencing technologies and simulates accordingly. It also uses context-dependent error profiles for realistic simulation…

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SimLoRD
Desktop

SimLoRD Simulation of Long Read Data

A Python-based read simulator whose error model corresponds to third-generation…

A Python-based read simulator whose error model corresponds to third-generation SMRT error characteristics, with default parameters based on public datasets. SimLoRD offers options to choose the read…

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FlowSim
Desktop

FlowSim

The commercial launch of 454 pyrosequencing in 2005 was a milestone in genome…

The commercial launch of 454 pyrosequencing in 2005 was a milestone in genome sequencing in terms of performance and cost. Flowsim is a simulator that generates realistic pyrosequencing data files of…

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PBSIM
Desktop

PBSIM

PacBio sequencers produce two types of characteristic reads (continuous long…

PacBio sequencers produce two types of characteristic reads (continuous long reads: long and high error rate and circular consensus sequencing: short and low error rate), both of which could be…

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ArtificialFastq…
Desktop

ArtificialFastqGenerator

Takes the reference genome (in FASTA format) as input and outputs artificial…

Takes the reference genome (in FASTA format) as input and outputs artificial FASTQ files in the Sanger format. It can accept Phred base quality scores from existing FASTQ files, and use them to…

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SiLiCO
Desktop

SiLiCO

Generates standardized sequencing results. SiLiCO simulates both PacBio and…

Generates standardized sequencing results. SiLiCO simulates both PacBio and Oxford Nanopore read sequencing results by stochastically generating genomic coordinates and extracting corresponding…

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Gargammel
Desktop

Gargammel

A set of programs aimed at simulating ancient DNA fragments. Gargamel can…

A set of programs aimed at simulating ancient DNA fragments. Gargamel can simulate most common features of a DNA sequences, including post-mortem DNA damage and base misincorporations. It simulates…

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CFSAN SNP…
Desktop

CFSAN SNP Mutator

Generates mutated sequence files from a reference genome. CFSAN SNP Mutator…

Generates mutated sequence files from a reference genome. CFSAN SNP Mutator reads a fasta file and generates any number of mutated fasta replicate files. It also generates a summary file listing the…

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Plantagora
Desktop

Plantagora

Leverages existing plant genome sequencing data to develop a web-based plant…

Leverages existing plant genome sequencing data to develop a web-based plant genome assembly simulation platform. For a given genome, a range of sequencing strategies were simulated and the resulting…

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Wessim
Desktop

Wessim

A targeted re-sequencing simulator that generates synthetic exome sequencing…

A targeted re-sequencing simulator that generates synthetic exome sequencing reads from a given sample genome. Wessim emulates conventional exome capture technologies, including Agilent's…

NGSphy
Desktop

NGSphy

Generates next generation sequencing (NGS) data from multiple loci. NGSphy aims…

Generates next generation sequencing (NGS) data from multiple loci. NGSphy aims to improve NGS phylogenomic pipeline. The software allows users to extract information of loci from several…

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CapSim
Desktop

CapSim

Simulates targeted capture sequencing data. CapSim simulates the dynamics of…

Simulates targeted capture sequencing data. CapSim simulates the dynamics of probe hybridisation in silico to generate a set of fragments to be sequenced. It emulates all various stages of the…

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TreeToReads
Desktop

TreeToReads

Generates raw read data from mutated genomes simulated under a known phylogeny.…

Generates raw read data from mutated genomes simulated under a known phylogeny. TreeToReads allows direct comparisons of simulated and observed data in a controlled environment. It allows researchers…

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NanoSim
Desktop

NanoSim

Captures the technology-specific features of Oxford Nanopore technologies (ONT)…

Captures the technology-specific features of Oxford Nanopore technologies (ONT) data and allows adjustments upon improvement of nanopore sequencing technology. NanoSim is a read simulator which…

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ReadSim
Desktop

ReadSim

A fast and simple read simulator to target long reads such as PacBio or…

A fast and simple read simulator to target long reads such as PacBio or Nanopore. ReadSim generates long reads mimicking the read length distribution present in an input file by selecting a random…

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CuReSim
Desktop
Web

CuReSim Customized Read Simulator

A customized tool which generates synthetic New-Generation Sequencing reads,…

A customized tool which generates synthetic New-Generation Sequencing reads, supporting read simulation for major letter-base sequencing platforms. CuReSim is developed in Java and is distributed as…

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simNGS
Desktop

simNGS

A software tool for simulating observations from Illumina sequencing machines…

A software tool for simulating observations from Illumina sequencing machines using the statistical models behind the AYB base-calling software. By default, observations only incorporate noise due to…

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Rose
Desktop

Rose

Implements a probabilistic model of the evolution of RNA-, DNA-, or…

Implements a probabilistic model of the evolution of RNA-, DNA-, or protein-like sequences. Rose allows for varying rates of mutation within the sequences, making it possible to establish so-called…

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FIGG
Desktop

FIGG Frequency-based Insilico Genome Generator

A large-scale whole genome simulation tool which generates large numbers of…

A large-scale whole genome simulation tool which generates large numbers of whole genomes with known sequence characteristics based on direct sampling of experimentally known or theorized variations.…

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FASTQSim
Desktop

FASTQSim

Enables users to assess the quality of NGS datasets. FASTQSim provides…

Enables users to assess the quality of NGS datasets. FASTQSim provides information about read length, read quality, repetitive and non-repetitive indel profiles, and single base pair substitutions.…

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XS
Desktop

XS

A skilled FASTQ read simulation tool, flexible, portable (does not need a…

A skilled FASTQ read simulation tool, flexible, portable (does not need a reference sequence) and tunable in terms of sequence complexity. XS handles Ion Torrent, Roche-454, Illumina and ABI-SOLiD…

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makenucseq
Desktop

makenucseq

Creates random nucleotide sequences. makenucseq writes an output file with a…

Creates random nucleotide sequences. makenucseq writes an output file with a set of random nucleotide sequences. The sequences are created with triplet frequencies matching those given in the file,…

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454sim
Desktop

454sim

An application for simulation of 454 data at high speed and accuracy. The…

An application for simulation of 454 data at high speed and accuracy. The program is multi-thread capable and is available as C++ source code or pre-compiled binaries. Sequence reads are simulated by…

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EAGLE
Desktop

EAGLE Enhanced Artificial Genome Engine

Designed to simulate the behaviour of Illumina's Next Generation…

Designed to simulate the behaviour of Illumina's Next Generation Sequencing instruments, in order to facilitate the development and testing of downstream applications.

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ShotGun
Desktop

ShotGun

A flexible short read simulator. ShotGun generates sequence data with…

A flexible short read simulator. ShotGun generates sequence data with user-specified read length and average depth, accommodates to cycle specific sequencing error rates, allows the read depth…

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simHTSD
Desktop

simHTSD simulate High-Throughput Sequencing Data

Given a reference sequence, it will create a large set of short nucleotide…

Given a reference sequence, it will create a large set of short nucleotide reads, simulating the output from today's high-throughput DNA sequencers, such as the Illumina Genome Analyzer II.

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Wgsim
Desktop

Wgsim

A small tool for simulating sequence reads from a reference genome. It is able…

A small tool for simulating sequence reads from a reference genome. It is able to simulate diploid genomes with SNPs and insertion/deletion (INDEL) polymorphisms, and simulate reads with uniform…

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Mason
Desktop

Mason

A read simulator software for Illumina, 454 and Sanger reads. Its features…

A read simulator software for Illumina, 454 and Sanger reads. Its features include position specific error rates and base quality values. Mason has been written with performance in mind and can…

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