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ART

Set of Simulation Tools

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.

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.

ART-ChocolateCherryCake-03-19-2015 (the latest version)

This is a minor maintenance release with two updates thanks to the feedback from Yancy Lo.

 

  • art_illumina, art_454, and art_SOLiD
    1. correct a typo in the HQ tag field of ART SAM alignment files
    2. 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.

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
    1. fix the issue that longer or shorter reads are produced in the new error-free SAM file when the original reads having indels
    2. fix the issue that generates empty reads when a reference sequence is too short by skipping the reference
    3. resolve the problem of doing endless looping when a reference sequence is much shorter than the defined mean fragment length
    4. fix a bug related to read length in ART_profiler_Illumina (thanks to Thomas Hack)
    5. add an option "-c --rcount" to specify #number of reads/read pairs to be simulated
    6. add built-in profiles of HiSeq1000 (100bp), HiSeq 2000(100bp) and HiSeq 2500(125bp and 150bp)
    7. add an option to specify a sequencing system of which a built-in profile is used for simulation
    8. 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.

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
    1. add the function of amplicon sequencing simulation
    2. add the support to generate sam file with zero-sequencing errors
    3. change the maximum allowed quality score to be 93 when scaling quality scores
    4. fix a bug related to simulation with a fixed random seed for paired-end simulation
    5. solve the crash issue when running on the newer MacOS X (10.9)
    6. allow reference sequences to be both DNA and RNA
    7. fix a bug related to masked 'N' regions when having multiple reference sequences
    8. add a cutoff frequency of "N"s of genomic regions for masking
    9. enable turning off the masking of 'N' regions
    10. other small improvements
  • art_454
    1. add amplicon sequencing simulation function
    2. allow reference sequences to be RNA sequences
    3. enable using a fixed random seed for simulation
    4. fix the paired-end read direction issue
    5. enhance log report and other improvements
  • art_SOLiD
    1. enable simulation with a fixed random seed to generate identical datasets from two simulations
    2. add support of F3-F5 paired-end read simulation
    3. add support of amplicon sequencing simulation
    4. allow reference sequences to be RNA
    5. enable simulation of reads up to 75bp in length with a testing error profile
    6. fix the issue of masking "N" genomic regions
    7. make it more user-friendly and some other improvements

 

Binary Packages

  Linux 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.

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-GrapeWine-08-15-2012

The release mainly fixed bugs for ART 454 simulator and added new features and functions as listed in the following:
  1. support GS FLX Titanium platform
  2. provide new built-in 454 read profiles for both GS FLX and GS FLX Titaium platforms
  3. add a new tool 454_readprofile_art that allows users to generate their own read profiles from new 454 read data
  4. add an option to change the default flow cycle number
  5. change to not output ALN files by default
  6. change the output of DNA sequences from lower case to upper case
  7. 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-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-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-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-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

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 Site . 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

 

  1. Single-end reads
    art_454 [ -s ] [ -p read_profile ] <INPUT_SEQ_FILE> <OUTPUT_FILE_PREFIX> <FOLD_COVERAGE>
    Example:
      art_454 seq_reference.fa ./outdir/dat_single_end 20
  2. Paired-end reads
    art_454 [ -s ] [ -p read_profile ] <INPUT_SEQ_FILE> <OUTPUT_FILE_PREFIX> <FOLD_COVERAGE> <MEAN_FRAG_LEN> <STD_DE>
    Example:
      art_454 seq_reference.fa ./outdir/dat_paired_end 20 500 20

 

Illumina read simulation

 

  1. Single-end reads
    art_illumina [options] -i <INPUT_SEQ_FILE> -l <READ_LEN> -f <FOLD_COVERAGE> -o <OUTPUT_FILE_PREFIX>
    Example:
      art_illumina -sam -i seq_reference.fa -l 50 -f 10 -o ./outdir/dat_single_end
  2. Paired-end reads
    art_illumina [options] -i <INPUT_SEQ_FILE> -l <READ_LEN> -f <FOLD_COVERAGE> -o <OUTPUT_FILE_PREFIX> -m <MEAN_FRAG_LEN> -s <STD_DE>
    Example:
      art_illumina -p -sam -i seq_reference.fa -l 50 -f 20 -m 200 -s 10 -o d./outdir/dat_paired_end
  3. Mate-pair reads
    art_illumina [options] -i <INPUT_SEQ_FILE> -l <READ_LEN> -f <FOLD_COVERAGE> -o <OUTPUT_FILE_PREFIX> -m <MEAN_FRAG_LEN> -s <STD_DE>
    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

 

  1. Single-end reads
    art_SOLiD [ -s ] [ -p read_profile ] <INPUT_SEQ_FILE> <OUTPUT_FILE_PREFIX> <READ_LEN> <FOLD_COVERAGE>
    Example:
      art_SOLiD -s seq_reference.fa ./outdir/dat_single_end 32 10
  2. Paired-end reads
    art_SOLiD [ -s ] [ -p read_profile ] <INPUT_SEQ_FILE> <OUTPUT_FILE_PREFIX> <READ_LEN> <FOLD_COVERAGE> <MEAN_FRAG_LEN> <STD_DE>
    Example:
       art_SOLiD seq_reference.fa ./outdir/dat_paired_end 25 10 500 20

Contact

Weichun Huang, Ph.D.
Weichun Huang, Ph.D.
Staff Scientist
Tel (919) 541-4943
huang6@niehs.nih.gov
P.O. Box 12233
Mail Drop A3-03
Research Triangle Park, NC 27709

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