GSR: Simulator - ART
Attribute | Value |
---|---|
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 | 7 years, 9 months ago |
Homepage | http://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 Certification | ✔ Accessibility |
Last evaluated | 01-09-2017 (2629 days ago) |
Attribute Category | Attribute |
---|---|
Target | |
Type of Simulated Data | Diploid DNA Sequence, Haploid DNA Sequence, Mitochondrial DNA, |
Variations | Genotype or Sequencing Error, |
Simulation Method | Other, |
Input | |
Data Type | Empirical, Ancestral Sequence, Reference genome, |
File format | Program Specific, Other, |
Output | |
Data Type | Genotype or Sequence, |
Sequencing Reads | Illumina, Roche 454, SOLiD, Other, |
File Format | Fasta or Fastq, SAM or BAM, Program Specific, |
Sample Type | Random 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 | |
Interface | Command-line, |
Development | |
Tested Platforms | Windows, Mac OS X, Linux and Unix, |
Language | C or C++, |
License | Other, |
GSR Certification | Accessibility, Documentation, Application, Support, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 7
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]