ART | National Institute of Environmental Health Sciences
Source: https://www.niehs.nih.gov/research/resources/software/biostatistics/art
Archived: 2026-04-23 17:14
ART | National Institute of Environmental Health Sciences
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ART
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Set of Simulation Tools
ART is 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 summarized from large recalibrated sequencing data. ART can also simulate reads using user own read error model or quality profiles. ART supports simulation of single-end, paired-end/mate-pair reads of three major commercial next-generation sequencing platforms: Illumina's Solexa, Roche's 454 and Applied Biosystems' SOLiD. ART can be used to test or benchmark a variety of method or tools for next-generation sequencing data analysis, including read alignment, de novo assembly, SNP and structure variation discovery. ART was used as a primary tool for the simulation study of the
1000 Genomes Project
. 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 format. ART can also generate alignments in the SAM alignment or UCSC BED file format. ART can be used together with genome variants simulators (e.g.
VarSim
) for evaluating variant calling tools or methods.
Availability
ART is freely available to public. The binary packages of ART are available for three major operating systems: Linux, Macintosh, and Windows. ART is also available as Platform-independent C++ source packages. Each package includes programs, documents and usage examples.
Citation
Weichun Huang, Leping Li, Jason R Myers, and Gabor T Marth. ART: a next-generation sequencing read simulator, Bioinformatics (2012) 28 (4): 593-594
ART-MountRainier-2016-06-05 (the latest version)
This is a minor maintenance release. Thanks to Rene Lujan and other users for their feedback.
fixed a bug leading to the indel rates of 2nd reads same as those of 1st reads
added a parameter to allow user to set the maximum number of insertions and deletions within a read
optimized insertion/deletion simulation
other minor changes
Binary Packages
Linux
MacOS X
Windows
64-bit system
ART-bin-MountRainier-2016.06.05-Linux64.tgz
(11MB)
ART-bin-MountRainier-2016.06.05-MacOS64.tgz
(4MB)
ART-bin-MountRainier-2016.06.05-Win64.zip
(5MB)
32-bit system
ART-bin-MountRainier-2016.06.05-Linux32.tgz
(6MB)
ART-bin-MountRainier-2016.06.05-MacOS32.tgz
(4MB)
ART-bin-MountRainier-2016.06.05-Win32.zip
(5MB)
Source Packages
all ART source codes are released as a single package. The MacOS and Linux source packages are for easy compilation in Mac and Linux OS, respectively. The same source codes can be compiled on Windows systems as well.
Linux OS:
ART-src-MountRainier-2016.06.05-Linux.tgz
(11MB)
Mac OS X:
ART-src-MountRainier-2016.06.05-MacOS.tgz
(10MB)
ART-GreatSmokyMountains-04-17-2016
This release added the support of the latest Illumina sequencing systems, fixed a crash bug, and made several other improvements as detailed below. While ART has always been free to the public, the release officially puts all ART codes under the
GPL version 3 license
. In addition, thanks to Andreas Tille and his Debian Med team, ART is in the process to be included in the Debian operating system. Thanks also to many users for their feedback.
added built-in quality profiles for the following Illumina sequencing systems
HSXn - HiSeqX PCR free, v2.5, 150bp
HSXt - HiSeqX TruSeq, v2.5, 150bp
MinS - MiniSeq TruSeq, 50bp, single-end only
MSv3 - MiSeq v3, 250bp
NS50 - NextSeq500 v2, 75bp
added the command line option to set the minimum (--minQ) and maximum (--maxQ) base quality scores for Illumina read simulation
fixed a bug related to the crash when simulating Illumina reads with a high error rate
updated illumina quality profile builder (art_profiler_illumina) to make it better and more robust The script now works on both MacOS and Linux/Unix systems, and allows users to set the number of threads to run the program
put all ART codes under
GPL version 3 license
made several other minor changes and enhancements
Binary Packages
Linux
MacOS X
Windows
64-bit system
ART-bin-GreatSmokyMountains-04.17.16-Linux64.tgz
(11MB)
ART-bin-GreatSmokyMountains-04.17.16-MacOS64.tgz
(4MB)
ART-bin-GreatSmokyMountains-04.17.16-Win64.zip
(5MB)
32-bit system
ART-bin-GreatSmokyMountains-04.17.16-Linux32.tgz
(6MB)
ART-bin-GreatSmokyMountains-04.17.16-MacOS32.tgz
(4MB)
ART-bin-GreatSmokyMountains-04.17.16-Win32.zip
(5MB)
Source Packages
All ART source codes are released as a single package. The MacOS and Linux source packages are for easy compilation in Mac and Linux OS, respectively. The same source codes can be compiled on Windows systems as well.
Linux OS:
ART-src-GreatSmokyMountains-04.17.16-Linux.tgz
(7MB)
Mac OS X:
ART-src-GreatSmokyMountains-04.17.16-MacOS.tgz
(6MB)
ART-ChocolateCherryCake-03-19-2015
This is a minor maintenance release with two updates thanks to the feedback from Yancy Lo.
art_illumina, art_454, and art_SOLiD
correct a typo in the HQ tag field of ART SAM alignment files
add an option to use 'M' instead of the default '=/X' for alignment match/mismatch CIGAR in ART SAM alignment files
Binary Packages
Linux
MacOS X
Windows
64-bit system
ART-bin-ChocolateCherryCake-03.19.15-Linux64.tgz
(9MB)
ART-bin-ChocolateCherryCake-03.19.15-MacOS64.tgz
(3MB)
ART-bin-ChocolateCherryCake-03.19.15-Win64.zip
(4MB)
32-bit system
ART-bin-ChocolateCherryCake-03.19.15-Linux32.tgz
(5MB)
ART-bin-ChocolateCherryCake-03.19.15-MacOS32.tgz
(3MB)
ART-bin-ChocolateCherryCake-03.19.15-Win32.zip
(4MB)
Source Packages
all ART source codes are now released as a single package. The MacOS and Linux source packages are for easy compilation in Mac and Linux OS, respectively. The source codes can be compiled on Windows systems as well.
Linux OS:
ART-src-ChocolateCherryCake-03.19.15-Linux.tgz
(10MB)
Mac OS X:
ART-src-ChocolateCherryCake-03.19.15-MacOS.tgz
(8MB)
ART-ChocolateCherries-03-09-2015
This release mainly updated ART Illumina simulator with all changes listed below. Thanks many users for their feedback and contributions to make the release possible.
art_illumina
fix the issue that longer or shorter reads are produced in the new error-free SAM file when the original reads having indels
fix the issue that generates empty reads when a reference sequence is too short by skipping the reference
resolve the problem of doing endless looping when a reference sequence is much shorter than the defined mean fragment length
fix a bug related to read length in ART_profiler_Illumina (thanks to Thomas Hack)
add an option "-c --rcount" to specify #number of reads/read pairs to be simulated
add built-in profiles of HiSeq1000 (100bp), HiSeq 2000(100bp) and HiSeq 2500(125bp and 150bp)
add an option to specify a sequencing system of which a built-in profile is used for simulation
report the sequencing system name used for simulation in ART output summary log
Binary Packages
Linux
MacOS X
Windows
64-bit system
ART-bin-ChocolateCherries-03.09.15-Linux64.tgz
(7MB)
ART-bin-ChocolateCherries-03.09.15-MacOS64.tgz
(3MB)
ART-bin-ChocolateCherries-03.09.15-Win64.zip
(6MB)
32-bit system
ART-bin-ChocolateCherries-03.09.15-Linux32.tgz
(5MB)
ART-bin-ChocolateCherries-03.09.15-MacOS32.tgz
(3MB)
ART-bin-ChocolateCherries-03.09.15-Win32.zip
(4MB)
Source Packages
all ART source codes are now released as a single package. The MacOS and Linux source packages are for easy compilation in Mac and Linux OS, respectively. The source codes can be compiled on Windows systems as well.
Linux OS:
ART-src-ChocolateCherries-03.09.15-Linux.tgz
(10MB)
Mac OS X:
ART-src-ChocolateCherries-03.09.15-MacOS.tgz
(8MB)
ART-VanillaIceCream-03-11-2014
This is a major update release including several new/enhanced features and bug fixes. All changes are listed blow. In addition, the accessory tools ART_profiler_454 and ART_profiler_illumina for ART read profile generation are included in each distribution package, so it is no need to download them separately. Thanks all users for their feedback and contributions that make the release possible.
art_illumina
add the function of amplicon sequencing simulation
add the support to generate sam file with zero-sequencing errors
change the maximum allowed quality score to be 93 when scaling quality scores
fix a bug related to simulation with a fixed random seed for paired-end simulation
solve the crash issue when running on the newer MacOS X (10.9)
allow reference sequences to be both DNA and RNA
fix a bug related to masked 'N' regions when having multiple reference sequences
add a cutoff frequency of "N"s of genomic regions for masking
enable turning off the masking of 'N' regions
other small improvements
art_454
add amplicon sequencing simulation function
allow reference sequences to be RNA sequences
enable using a fixed random seed for simulation
fix the paired-end read direction issue
enhance log report and other improvements
art_SOLiD
enable simulation with a fixed random seed to generate identical datasets from two simulations
add support of F3-F5 paired-end read simulation
add support of amplicon sequencing simulation
allow reference sequences to be RNA
enable simulation of reads up to 75bp in length with a testing error profile
fix the issue of masking "N" genomic regions
make it more user-friendly and some other improvements
Binary Packages
Linux
data-sortable="false">
MacOS X
Windows
64-bit system
ART-bin-VanillaIceCream-03.11.14-Linux64.tgz
(5MB)
ART-bin-VanillaIceCream-03.11.14-MacOS64.tgz
(2MB)
ART-bin-VanillaIceCream-03.11.14-Win64.zip
(6MB)
32-bit system
ART-bin-VanillaIceCream-03.11.14-Linux32.tgz
(4MB)
ART-bin-VanillaIceCream-03.11.14-MacOS32.tgz
(2MB)
ART-bin-VanillaIceCream-03.11.14-Win32.zip
(3MB)
Source Packages
all ART source codes are now released as a single package. The MacOS and Linux source packages are for easy compilation in Mac and Linux OS, respectively. The source codes can be compiled on Windows systems as well.
Linux OS:
ART-src-VanillaIceCream-03.11.14-Linux.tgz
(8MB)
Mac OS X:
ART-src-VanillaIceCream-03.11.14-MacOS.tgz
(7MB)
ART-BananaPancakes-04-02-2013
The release mainly fixed a bug related to "noALN" option for ART Illumina simulator and added a built-in MiSeq 250bp read profile
Binary Packages
Linux
MacOS X
Windows
64-bit system
art-all-Linux64-bin_BP.tar.gz
(5MB)
art-all-MacOS64-bin_BP.tar.gz
(2MB)
art-all-Win64-bin_BP.zip
(5MB)
32-bit system
art-all-Linux32-bin_BP.tar.gz
(4MB)
art-all-MacOS32-bin_BP.tar.gz
(2MB)
art-all-Win32-bin_BP.zip
(2MB)
Source Packages
ART Illumina read simulator
art_Illumina_src-1.5.1.tar.gz
(4MB)
ART 454 read simulator
art_454_src-2.1.8.tar.gz
(3MB)
(no updates)
ART SOLiD read simulator
art_SOLiD_src-1.0.1.tar.gz
(2MB)
(no updates)
ART-GrapeWine-08-15-2012
The release mainly fixed bugs for ART 454 simulator and added new features and functions as listed in the following:
support GS FLX Titanium platform
provide new built-in 454 read profiles for both GS FLX and GS FLX Titaium platforms
add a new tool 454_readprofile_art that allows users to generate their own read profiles from new 454 read data
add an option to change the default flow cycle number
change to not output ALN files by default
change the output of DNA sequences from lower case to upper case
switch automatically to the default indel error profile when user own profile does not provide it
Binary Packages
Linux
MacOS X
Windows
64-bit system
art-all-Linux64-bin_GW.tar.gz
(6MB)
art-all-MacOS64-bin_GW.tar.gz
(2MB)
art-all-Win64-bin_GW.zip
(5MB)
32-bit system
art-all-Linux32-bin_GW.tar.gz
(3MB)
art-all-MacOS32-bin_GW.tar.gz
(2MB)
art-all-Win32-bin_GW.zip
(1MB)
Source Packages
ART Illumina read simulator
art_Illumina_src-1.5.0.tar.gz (no updates)
(5MB)
ART 454 read simulator
art_454_src-2.1.8.tar.gz
(3MB)
ART SOLiD read simulator
art_SOLiD_src-1.0.1.tar.gz
(2MB)
ART-PeachPie-05-16-2012
Binary Packages
Linux
MacOS X
Windows
64-bit system
art-all-Linux64-bin_PP.tar.gz
(4MB)
art-all-MacOS64-bin_PP.tar.gz
(1MB)
art-all-Win64-bin_PP.zip
(4MB)
32-bit system
art-all-Linux32-bin_PP.tar.gz
(3MB)
art-all-MacOS32-bin_PP.tar.gz
(1MB)
art-all-Win32-bin_PP.zip
(1MB)
Source Packages
ART Illumina read simulator
art_Illumina_src-1.5.0.tar.gz
(5MB)
ART 454 read simulator
art_454_src-1.6.8.tar.gz (no updates)
(2MB)
ART SOLiD read simulator
art_SOLiD_src-1.0.1.tar.gz (no updates)
(2MB)
ART-CoconutCoffee-01-10-2012
Binary Packages
Linux
MacOS X
Windows
64-bit system
art-all-Linux64-bin_CC.tar.gz
(3MB)
art-all-MacOS64-bin_CC.tar.gz
(1MB)
art-all-Win64-bin_CC.zip
(4MB)
32-bit system
art-all-Linux32-bin_CC.tar.gz
(3MB)
art-all-MacOS32-bin_CC.tar.gz
(1MB)
art-all-Win32-bin_CC.zip
(1MB)
Source Packages
ART Illumina read simulator
art_Illumina_src-1.3.6.tar.gz
(5MB)
ART 454 read simulator
art_454_src-1.6.8.tar.gz (no updates)
(2MB)
ART SOLiD read simulator
art_SOLiD_src-1.0.1.tar.gz (no updates)
(2MB)
ART-CranberryJuice-11-23-2011
Binary Packages
Linux
MacOS X
Windows
64-bit system
art-all-Linux64-bin_CJ.tar.gz
(3MB)
art-all-MacOS64-bin_CJ.tar.gz
(1MB)
art-all-Win64-bin_CJ.tar.gz.zip
(4MB)
32-bit system
art-all-Linux32-bin_CJ.tar.gz
(2MB)
art-all-MacOS32-bin_CJ.tar.gz
(1MB)
art-all-Win32-bin_CJ.tar.gz.zip
(1MB)
Source Packages
ART 454 read simulator
art_454_src-1.6.8.tar.gz
(2MB)
ART Illumina read simulator
art_Illumina_src-1.3.1.tar.gz
(4MB)
ART SOLiD read simulator
art_SOLiD_src-1.0.1.tar.gz
(2MB)
ART-ApplePie-04-21-2011
Binary Packages
Linux
MacOS X
Windows
64-bit system
art-all-Linux64-bin_AP.tar.gz
(3MB)
art-all-MacOS64-bin_AP.tar.gz
(1MB)
art-all-Win64-bin_AP.tar.gz.zip
(4MB)
32-bit system
art-all-Linux32-bin_AP.tar.gz
(2MB)
art-all-MacOS32-bin_AP.tar.gz
(1MB)
art-all-Win32-bin_AP.tar.gz.zip
(1MB)
Source Packages
ART 454 read simulator
art_454_src-1.2.5.tar.gz
(877KB)
ART Illumina read simulator
art_Illumina_src-1.1.5.tar.gz
(2MB)
ART SOLiD read simulator
art_SOLiD_src-0.9.1.tar.gz
(1023KB)
Installation
Compilation and installation from a source package
Compilation of ART from its source codes requires the GNU Scientific Library (GSL). The GSL can be freely downloaded from GNU at
GSL Software Website
. To compile under a Linux/Unix-like operating system, please first download and unpack a desired source package, then enter the first directory of the unpacked package, and issue the following commands:
./configure
make
make install
Installation from a binary package
Installation is to simply unpack the binary package to your installation directory. The executable programs are art_454, art_illumina, and art_SOLiD for 454, Illumina, and SOLiD platforms, respectively. Under Linux or MacOS, please use the following command to unpack a *.tar.gz binary package:
tar xfz art_*.tar.gz
ART binary package for Windows OS is in a ZIP package. You can right click a ZIP package, and click "extract" in the context-menu to unpack the package.
Usages
Simple ART usages and examples are given below. Please refer to the README file in each distribution package for examples and other detail documentation.
454 read simulation
Single-end reads
art_454 [ -s ] [ -p read_profile ]
Example:
art_454 seq_reference.fa ./outdir/dat_single_end 20
Paired-end reads
art_454 [ -s ] [ -p read_profile ]
Example:
art_454 seq_reference.fa ./outdir/dat_paired_end 20 500 20
Illumina read simulation
Single-end reads
art_illumina [options] -i -l -f -o
Example:
art_illumina -sam -i seq_reference.fa -l 50 -f 10 -o ./outdir/dat_single_end
Paired-end reads
art_illumina [options] -i -l -f -o -m -s
Example:
art_illumina -p -sam -i seq_reference.fa -l 50 -f 20 -m 200 -s 10 -o d./outdir/dat_paired_end
Mate-pair reads
art_illumina [options] -i -l -f -o -m -s
Example:
art_illumina -mp -sam -i seq_reference.fa -l 50 -f 20 -m 2050 -s 50 -o d./outdir/dat_paired_end
SOLiD read simulation
Single-end reads
art_SOLiD [ -s ] [ -p read_profile ]
Example:
art_SOLiD -s seq_reference.fa ./outdir/dat_single_end 32 10
Paired-end reads
art_SOLiD [ -s ] [ -p read_profile ]
Example:
art_SOLiD seq_reference.fa ./outdir/dat_paired_end 25 10 500 20
Back
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Last Reviewed: December 31, 2025
Skip Navigation
ART
Close the left navigation
Add
Set of Simulation Tools
ART is 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 summarized from large recalibrated sequencing data. ART can also simulate reads using user own read error model or quality profiles. ART supports simulation of single-end, paired-end/mate-pair reads of three major commercial next-generation sequencing platforms: Illumina's Solexa, Roche's 454 and Applied Biosystems' SOLiD. ART can be used to test or benchmark a variety of method or tools for next-generation sequencing data analysis, including read alignment, de novo assembly, SNP and structure variation discovery. ART was used as a primary tool for the simulation study of the
1000 Genomes Project
. 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 format. ART can also generate alignments in the SAM alignment or UCSC BED file format. ART can be used together with genome variants simulators (e.g.
VarSim
) for evaluating variant calling tools or methods.
Availability
ART is freely available to public. The binary packages of ART are available for three major operating systems: Linux, Macintosh, and Windows. ART is also available as Platform-independent C++ source packages. Each package includes programs, documents and usage examples.
Citation
Weichun Huang, Leping Li, Jason R Myers, and Gabor T Marth. ART: a next-generation sequencing read simulator, Bioinformatics (2012) 28 (4): 593-594
ART-MountRainier-2016-06-05 (the latest version)
This is a minor maintenance release. Thanks to Rene Lujan and other users for their feedback.
fixed a bug leading to the indel rates of 2nd reads same as those of 1st reads
added a parameter to allow user to set the maximum number of insertions and deletions within a read
optimized insertion/deletion simulation
other minor changes
Binary Packages
Linux
MacOS X
Windows
64-bit system
ART-bin-MountRainier-2016.06.05-Linux64.tgz
(11MB)
ART-bin-MountRainier-2016.06.05-MacOS64.tgz
(4MB)
ART-bin-MountRainier-2016.06.05-Win64.zip
(5MB)
32-bit system
ART-bin-MountRainier-2016.06.05-Linux32.tgz
(6MB)
ART-bin-MountRainier-2016.06.05-MacOS32.tgz
(4MB)
ART-bin-MountRainier-2016.06.05-Win32.zip
(5MB)
Source Packages
all ART source codes are released as a single package. The MacOS and Linux source packages are for easy compilation in Mac and Linux OS, respectively. The same source codes can be compiled on Windows systems as well.
Linux OS:
ART-src-MountRainier-2016.06.05-Linux.tgz
(11MB)
Mac OS X:
ART-src-MountRainier-2016.06.05-MacOS.tgz
(10MB)
ART-GreatSmokyMountains-04-17-2016
This release added the support of the latest Illumina sequencing systems, fixed a crash bug, and made several other improvements as detailed below. While ART has always been free to the public, the release officially puts all ART codes under the
GPL version 3 license
. In addition, thanks to Andreas Tille and his Debian Med team, ART is in the process to be included in the Debian operating system. Thanks also to many users for their feedback.
added built-in quality profiles for the following Illumina sequencing systems
HSXn - HiSeqX PCR free, v2.5, 150bp
HSXt - HiSeqX TruSeq, v2.5, 150bp
MinS - MiniSeq TruSeq, 50bp, single-end only
MSv3 - MiSeq v3, 250bp
NS50 - NextSeq500 v2, 75bp
added the command line option to set the minimum (--minQ) and maximum (--maxQ) base quality scores for Illumina read simulation
fixed a bug related to the crash when simulating Illumina reads with a high error rate
updated illumina quality profile builder (art_profiler_illumina) to make it better and more robust The script now works on both MacOS and Linux/Unix systems, and allows users to set the number of threads to run the program
put all ART codes under
GPL version 3 license
made several other minor changes and enhancements
Binary Packages
Linux
MacOS X
Windows
64-bit system
ART-bin-GreatSmokyMountains-04.17.16-Linux64.tgz
(11MB)
ART-bin-GreatSmokyMountains-04.17.16-MacOS64.tgz
(4MB)
ART-bin-GreatSmokyMountains-04.17.16-Win64.zip
(5MB)
32-bit system
ART-bin-GreatSmokyMountains-04.17.16-Linux32.tgz
(6MB)
ART-bin-GreatSmokyMountains-04.17.16-MacOS32.tgz
(4MB)
ART-bin-GreatSmokyMountains-04.17.16-Win32.zip
(5MB)
Source Packages
All ART source codes are released as a single package. The MacOS and Linux source packages are for easy compilation in Mac and Linux OS, respectively. The same source codes can be compiled on Windows systems as well.
Linux OS:
ART-src-GreatSmokyMountains-04.17.16-Linux.tgz
(7MB)
Mac OS X:
ART-src-GreatSmokyMountains-04.17.16-MacOS.tgz
(6MB)
ART-ChocolateCherryCake-03-19-2015
This is a minor maintenance release with two updates thanks to the feedback from Yancy Lo.
art_illumina, art_454, and art_SOLiD
correct a typo in the HQ tag field of ART SAM alignment files
add an option to use 'M' instead of the default '=/X' for alignment match/mismatch CIGAR in ART SAM alignment files
Binary Packages
Linux
MacOS X
Windows
64-bit system
ART-bin-ChocolateCherryCake-03.19.15-Linux64.tgz
(9MB)
ART-bin-ChocolateCherryCake-03.19.15-MacOS64.tgz
(3MB)
ART-bin-ChocolateCherryCake-03.19.15-Win64.zip
(4MB)
32-bit system
ART-bin-ChocolateCherryCake-03.19.15-Linux32.tgz
(5MB)
ART-bin-ChocolateCherryCake-03.19.15-MacOS32.tgz
(3MB)
ART-bin-ChocolateCherryCake-03.19.15-Win32.zip
(4MB)
Source Packages
all ART source codes are now released as a single package. The MacOS and Linux source packages are for easy compilation in Mac and Linux OS, respectively. The source codes can be compiled on Windows systems as well.
Linux OS:
ART-src-ChocolateCherryCake-03.19.15-Linux.tgz
(10MB)
Mac OS X:
ART-src-ChocolateCherryCake-03.19.15-MacOS.tgz
(8MB)
ART-ChocolateCherries-03-09-2015
This release mainly updated ART Illumina simulator with all changes listed below. Thanks many users for their feedback and contributions to make the release possible.
art_illumina
fix the issue that longer or shorter reads are produced in the new error-free SAM file when the original reads having indels
fix the issue that generates empty reads when a reference sequence is too short by skipping the reference
resolve the problem of doing endless looping when a reference sequence is much shorter than the defined mean fragment length
fix a bug related to read length in ART_profiler_Illumina (thanks to Thomas Hack)
add an option "-c --rcount" to specify #number of reads/read pairs to be simulated
add built-in profiles of HiSeq1000 (100bp), HiSeq 2000(100bp) and HiSeq 2500(125bp and 150bp)
add an option to specify a sequencing system of which a built-in profile is used for simulation
report the sequencing system name used for simulation in ART output summary log
Binary Packages
Linux
MacOS X
Windows
64-bit system
ART-bin-ChocolateCherries-03.09.15-Linux64.tgz
(7MB)
ART-bin-ChocolateCherries-03.09.15-MacOS64.tgz
(3MB)
ART-bin-ChocolateCherries-03.09.15-Win64.zip
(6MB)
32-bit system
ART-bin-ChocolateCherries-03.09.15-Linux32.tgz
(5MB)
ART-bin-ChocolateCherries-03.09.15-MacOS32.tgz
(3MB)
ART-bin-ChocolateCherries-03.09.15-Win32.zip
(4MB)
Source Packages
all ART source codes are now released as a single package. The MacOS and Linux source packages are for easy compilation in Mac and Linux OS, respectively. The source codes can be compiled on Windows systems as well.
Linux OS:
ART-src-ChocolateCherries-03.09.15-Linux.tgz
(10MB)
Mac OS X:
ART-src-ChocolateCherries-03.09.15-MacOS.tgz
(8MB)
ART-VanillaIceCream-03-11-2014
This is a major update release including several new/enhanced features and bug fixes. All changes are listed blow. In addition, the accessory tools ART_profiler_454 and ART_profiler_illumina for ART read profile generation are included in each distribution package, so it is no need to download them separately. Thanks all users for their feedback and contributions that make the release possible.
art_illumina
add the function of amplicon sequencing simulation
add the support to generate sam file with zero-sequencing errors
change the maximum allowed quality score to be 93 when scaling quality scores
fix a bug related to simulation with a fixed random seed for paired-end simulation
solve the crash issue when running on the newer MacOS X (10.9)
allow reference sequences to be both DNA and RNA
fix a bug related to masked 'N' regions when having multiple reference sequences
add a cutoff frequency of "N"s of genomic regions for masking
enable turning off the masking of 'N' regions
other small improvements
art_454
add amplicon sequencing simulation function
allow reference sequences to be RNA sequences
enable using a fixed random seed for simulation
fix the paired-end read direction issue
enhance log report and other improvements
art_SOLiD
enable simulation with a fixed random seed to generate identical datasets from two simulations
add support of F3-F5 paired-end read simulation
add support of amplicon sequencing simulation
allow reference sequences to be RNA
enable simulation of reads up to 75bp in length with a testing error profile
fix the issue of masking "N" genomic regions
make it more user-friendly and some other improvements
Binary Packages
Linux
data-sortable="false">
MacOS X
Windows
64-bit system
ART-bin-VanillaIceCream-03.11.14-Linux64.tgz
(5MB)
ART-bin-VanillaIceCream-03.11.14-MacOS64.tgz
(2MB)
ART-bin-VanillaIceCream-03.11.14-Win64.zip
(6MB)
32-bit system
ART-bin-VanillaIceCream-03.11.14-Linux32.tgz
(4MB)
ART-bin-VanillaIceCream-03.11.14-MacOS32.tgz
(2MB)
ART-bin-VanillaIceCream-03.11.14-Win32.zip
(3MB)
Source Packages
all ART source codes are now released as a single package. The MacOS and Linux source packages are for easy compilation in Mac and Linux OS, respectively. The source codes can be compiled on Windows systems as well.
Linux OS:
ART-src-VanillaIceCream-03.11.14-Linux.tgz
(8MB)
Mac OS X:
ART-src-VanillaIceCream-03.11.14-MacOS.tgz
(7MB)
ART-BananaPancakes-04-02-2013
The release mainly fixed a bug related to "noALN" option for ART Illumina simulator and added a built-in MiSeq 250bp read profile
Binary Packages
Linux
MacOS X
Windows
64-bit system
art-all-Linux64-bin_BP.tar.gz
(5MB)
art-all-MacOS64-bin_BP.tar.gz
(2MB)
art-all-Win64-bin_BP.zip
(5MB)
32-bit system
art-all-Linux32-bin_BP.tar.gz
(4MB)
art-all-MacOS32-bin_BP.tar.gz
(2MB)
art-all-Win32-bin_BP.zip
(2MB)
Source Packages
ART Illumina read simulator
art_Illumina_src-1.5.1.tar.gz
(4MB)
ART 454 read simulator
art_454_src-2.1.8.tar.gz
(3MB)
(no updates)
ART SOLiD read simulator
art_SOLiD_src-1.0.1.tar.gz
(2MB)
(no updates)
ART-GrapeWine-08-15-2012
The release mainly fixed bugs for ART 454 simulator and added new features and functions as listed in the following:
support GS FLX Titanium platform
provide new built-in 454 read profiles for both GS FLX and GS FLX Titaium platforms
add a new tool 454_readprofile_art that allows users to generate their own read profiles from new 454 read data
add an option to change the default flow cycle number
change to not output ALN files by default
change the output of DNA sequences from lower case to upper case
switch automatically to the default indel error profile when user own profile does not provide it
Binary Packages
Linux
MacOS X
Windows
64-bit system
art-all-Linux64-bin_GW.tar.gz
(6MB)
art-all-MacOS64-bin_GW.tar.gz
(2MB)
art-all-Win64-bin_GW.zip
(5MB)
32-bit system
art-all-Linux32-bin_GW.tar.gz
(3MB)
art-all-MacOS32-bin_GW.tar.gz
(2MB)
art-all-Win32-bin_GW.zip
(1MB)
Source Packages
ART Illumina read simulator
art_Illumina_src-1.5.0.tar.gz (no updates)
(5MB)
ART 454 read simulator
art_454_src-2.1.8.tar.gz
(3MB)
ART SOLiD read simulator
art_SOLiD_src-1.0.1.tar.gz
(2MB)
ART-PeachPie-05-16-2012
Binary Packages
Linux
MacOS X
Windows
64-bit system
art-all-Linux64-bin_PP.tar.gz
(4MB)
art-all-MacOS64-bin_PP.tar.gz
(1MB)
art-all-Win64-bin_PP.zip
(4MB)
32-bit system
art-all-Linux32-bin_PP.tar.gz
(3MB)
art-all-MacOS32-bin_PP.tar.gz
(1MB)
art-all-Win32-bin_PP.zip
(1MB)
Source Packages
ART Illumina read simulator
art_Illumina_src-1.5.0.tar.gz
(5MB)
ART 454 read simulator
art_454_src-1.6.8.tar.gz (no updates)
(2MB)
ART SOLiD read simulator
art_SOLiD_src-1.0.1.tar.gz (no updates)
(2MB)
ART-CoconutCoffee-01-10-2012
Binary Packages
Linux
MacOS X
Windows
64-bit system
art-all-Linux64-bin_CC.tar.gz
(3MB)
art-all-MacOS64-bin_CC.tar.gz
(1MB)
art-all-Win64-bin_CC.zip
(4MB)
32-bit system
art-all-Linux32-bin_CC.tar.gz
(3MB)
art-all-MacOS32-bin_CC.tar.gz
(1MB)
art-all-Win32-bin_CC.zip
(1MB)
Source Packages
ART Illumina read simulator
art_Illumina_src-1.3.6.tar.gz
(5MB)
ART 454 read simulator
art_454_src-1.6.8.tar.gz (no updates)
(2MB)
ART SOLiD read simulator
art_SOLiD_src-1.0.1.tar.gz (no updates)
(2MB)
ART-CranberryJuice-11-23-2011
Binary Packages
Linux
MacOS X
Windows
64-bit system
art-all-Linux64-bin_CJ.tar.gz
(3MB)
art-all-MacOS64-bin_CJ.tar.gz
(1MB)
art-all-Win64-bin_CJ.tar.gz.zip
(4MB)
32-bit system
art-all-Linux32-bin_CJ.tar.gz
(2MB)
art-all-MacOS32-bin_CJ.tar.gz
(1MB)
art-all-Win32-bin_CJ.tar.gz.zip
(1MB)
Source Packages
ART 454 read simulator
art_454_src-1.6.8.tar.gz
(2MB)
ART Illumina read simulator
art_Illumina_src-1.3.1.tar.gz
(4MB)
ART SOLiD read simulator
art_SOLiD_src-1.0.1.tar.gz
(2MB)
ART-ApplePie-04-21-2011
Binary Packages
Linux
MacOS X
Windows
64-bit system
art-all-Linux64-bin_AP.tar.gz
(3MB)
art-all-MacOS64-bin_AP.tar.gz
(1MB)
art-all-Win64-bin_AP.tar.gz.zip
(4MB)
32-bit system
art-all-Linux32-bin_AP.tar.gz
(2MB)
art-all-MacOS32-bin_AP.tar.gz
(1MB)
art-all-Win32-bin_AP.tar.gz.zip
(1MB)
Source Packages
ART 454 read simulator
art_454_src-1.2.5.tar.gz
(877KB)
ART Illumina read simulator
art_Illumina_src-1.1.5.tar.gz
(2MB)
ART SOLiD read simulator
art_SOLiD_src-0.9.1.tar.gz
(1023KB)
Installation
Compilation and installation from a source package
Compilation of ART from its source codes requires the GNU Scientific Library (GSL). The GSL can be freely downloaded from GNU at
GSL Software Website
. To compile under a Linux/Unix-like operating system, please first download and unpack a desired source package, then enter the first directory of the unpacked package, and issue the following commands:
./configure
make
make install
Installation from a binary package
Installation is to simply unpack the binary package to your installation directory. The executable programs are art_454, art_illumina, and art_SOLiD for 454, Illumina, and SOLiD platforms, respectively. Under Linux or MacOS, please use the following command to unpack a *.tar.gz binary package:
tar xfz art_*.tar.gz
ART binary package for Windows OS is in a ZIP package. You can right click a ZIP package, and click "extract" in the context-menu to unpack the package.
Usages
Simple ART usages and examples are given below. Please refer to the README file in each distribution package for examples and other detail documentation.
454 read simulation
Single-end reads
art_454 [ -s ] [ -p read_profile ]
Example:
art_454 seq_reference.fa ./outdir/dat_single_end 20
Paired-end reads
art_454 [ -s ] [ -p read_profile ]
Example:
art_454 seq_reference.fa ./outdir/dat_paired_end 20 500 20
Illumina read simulation
Single-end reads
art_illumina [options] -i
Example:
art_illumina -sam -i seq_reference.fa -l 50 -f 10 -o ./outdir/dat_single_end
Paired-end reads
art_illumina [options] -i
Example:
art_illumina -p -sam -i seq_reference.fa -l 50 -f 20 -m 200 -s 10 -o d./outdir/dat_paired_end
Mate-pair reads
art_illumina [options] -i
Example:
art_illumina -mp -sam -i seq_reference.fa -l 50 -f 20 -m 2050 -s 50 -o d./outdir/dat_paired_end
SOLiD read simulation
Single-end reads
art_SOLiD [ -s ] [ -p read_profile ]
Example:
art_SOLiD -s seq_reference.fa ./outdir/dat_single_end 32 10
Paired-end reads
art_SOLiD [ -s ] [ -p read_profile ]
Example:
art_SOLiD seq_reference.fa ./outdir/dat_paired_end 25 10 500 20
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Last Reviewed: December 31, 2025