GSR: Simulator - ART

Basic Package Attributes
AttributeValue
Title ART
Short Description 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.
Long Description 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. ART supports simulation of single-end, paired-end and mate-pair reads of three major commercial next-generation sequencing platforms: Illumina's Solexa, Roche's 454 and Applied Biosystems' SOLiD. ART can perform regular genome sequencing simulation as well amplicon sequencing simulation. ART is implemented in C++ with optimized algorithms and is highly efficient in read simulation. ART outputs reads in the FASTQ format, and alignments in the ALN/MAP and/or SAM format. ART can also generate alignments in UCSC BED file format.
Version ART-MountRainier-2016-06-05
Project Started 2011
Last Release 4 years, 4 months ago
Homepagehttp://www.niehs.nih.gov/research/resources/software/biostatistics/art/
Citations Huang W, Li L, Myers JR, Marth GT, ART: a next-generation sequencing read simulator., Bioinformatics, 02-15-2012 [ Abstract, cited in PMC ]
GSR CertificationGSR-certified

Accessibility
Documentation
Application
Support

Last evaluated01-09-2017 (1376 days ago)
Detailed Attributes
Attribute CategoryAttribute
Target
Type of Simulated DataDiploid DNA Sequence, Haploid DNA Sequence, Mitochondrial DNA,
VariationsGenotype or Sequencing Error,
Simulation MethodOther,
Input
Data TypeEmpirical, Ancestral Sequence, Reference genome,
File formatProgram Specific, Other,
Output
Data TypeGenotype or Sequence,
Sequencing ReadsIllumina, Roche 454, SOLiD, Other,
File FormatFasta or Fastq, SAM or BAM, Program Specific,
Sample TypeRandom or Independent,
Phenotype
Trait Type
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
InterfaceCommand-line,
Development
Tested PlatformsWindows, Mac OS X, Linux and Unix,
LanguageC or C++,
LicenseOther,
GSR CertificationAccessibility, Documentation, Application, Support,

The following 7 publications are selected examples of applications that used ART.

2016

Sessegolo C, Burlet N, Haudry A, Strong phylogenetic inertia on genome size and transposable element content among 26 species of flies., Biol Lett, 08-01-2016 [Abstract]

Hutchinson S, Glover L, Horn D, High-resolution analysis of multi-copy variant surface glycoprotein gene expression sites in African trypanosomes., BMC Genomics, 10-18-2016 [Abstract]

Faksri K, Xia E, Tan JH, Teo YY, Ong RT, In silico region of difference (RD) analysis of Mycobacterium tuberculosis complex from sequence reads using RD-Analyzer., BMC Genomics, 11-02-2016 [Abstract]

DeMaere MZ, Darling AE, Deconvoluting simulated metagenomes: the performance of hard- and soft- clustering algorithms applied to metagenomic chromosome conformation capture (3C)., PeerJ, 11-08-2016 [Abstract]

Lux M, Krüger J, Rinke C, Maus I, Schlüter A, Woyke T, Sczyrba A, Hammer B, acdc - Automated Contamination Detection and Confidence estimation for single-cell genome data., BMC Bioinformatics, 12-20-2016 [Abstract]

2014

Zhang J, Kobert K, Flouri T, Stamatakis A, PEAR: a fast and accurate Illumina Paired-End reAd mergeR., Bioinformatics, 03-01-2014 [Abstract]

2013

Liao Y, Smyth GK, Shi W, The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote., Nucleic Acids Res, 05-01-2013 [Abstract]


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