ART

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.

Citation

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 readsadded a parameter to allow user to set the maximum number of insertions and deletions within a readoptimized insertion/deletion simulationother minor changesBinary PackagesLinuxMacOS XWindows64-bit system 32-bit system Source Packagesall 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: Mac OS X:

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 systemsHSXn - HiSeqX PCR free, v2.5, 150bpHSXt - HiSeqX TruSeq, v2.5, 150bpMinS - MiniSeq TruSeq, 50bp, single-end onlyMSv3 - MiSeq v3, 250bpNS50 - NextSeq500 v2, 75bpadded the command line option to set the minimum (--minQ) and maximum (--maxQ) base quality scores for Illumina read simulationfixed a bug related to the crash when simulating Illumina reads with a high error rateupdated 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 programput all ART codes under GPL version 3 licensemade several other minor changes and enhancementsBinary PackagesLinuxMacOS XWindows64-bit system 32-bit system Source PackagesAll 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: Mac OS X:

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_SOLiDcorrect a typo in the HQ tag field of ART SAM alignment filesadd an option to use 'M' instead of the default '=/X' for alignment match/mismatch CIGAR in ART SAM alignment filesBinary PackagesLinuxMacOS XWindows64-bit system 32-bit system Source Packagesall 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: Mac OS X:

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_illuminafix the issue that longer or shorter reads are produced in the new error-free SAM file when the original reads having indelsfix the issue that generates empty reads when a reference sequence is too short by skipping the referenceresolve the problem of doing endless looping when a reference sequence is much shorter than the defined mean fragment lengthfix 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 simulatedadd 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 simulationreport the sequencing system name used for simulation in ART output summary logBinary PackagesLinuxMacOS XWindows64-bit system 32-bit system Source Packagesall 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: Mac OS X:

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_illuminaadd the function of amplicon sequencing simulationadd the support to generate sam file with zero-sequencing errorschange the maximum allowed quality score to be 93 when scaling quality scoresfix a bug related to simulation with a fixed random seed for paired-end simulationsolve the crash issue when running on the newer MacOS X (10.9)allow reference sequences to be both DNA and RNAfix a bug related to masked 'N' regions when having multiple reference sequencesadd a cutoff frequency of "N"s of genomic regions for maskingenable turning off the masking of 'N' regionsother small improvementsart_454add amplicon sequencing simulation functionallow reference sequences to be RNA sequencesenable using a fixed random seed for simulationfix the paired-end read direction issueenhance log report and other improvementsart_SOLiDenable simulation with a fixed random seed to generate identical datasets from two simulationsadd support of F3-F5 paired-end read simulationadd support of amplicon sequencing simulationallow reference sequences to be RNAenable simulation of reads up to 75bp in length with a testing error profilefix the issue of masking "N" genomic regionsmake it more user-friendly and some other improvementsBinary PackagesLinuxdata-sortable="false">MacOS XWindows64-bit system 32-bit system Source Packagesall 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: Mac OS X:

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 profileBinary PackagesLinuxMacOS XWindows64-bit system 32-bit system Source PackagesART Illumina read simulator ART 454 read simulator (no updates)ART SOLiD read simulator (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 platformprovide new built-in 454 read profiles for both GS FLX and GS FLX Titaium platformsadd a new tool 454_readprofile_art that allows users to generate their own read profiles from new 454 read dataadd an option to change the default flow cycle numberchange to not output ALN files by defaultchange the output of DNA sequences from lower case to upper caseswitch automatically to the default indel error profile when user own profile does not provide itBinary PackagesLinuxMacOS XWindows64-bit system 32-bit system Source PackagesART Illumina read simulator ART 454 read simulator ART SOLiD read simulator

ART-PeachPie-05-16-2012

Binary PackagesLinuxMacOS XWindows64-bit system 32-bit system Source PackagesART Illumina read simulator ART 454 read simulator ART SOLiD read simulator

ART-CoconutCoffee-01-10-2012

Binary PackagesLinuxMacOS XWindows64-bit system 32-bit system Source PackagesART Illumina read simulator ART 454 read simulator ART SOLiD read simulator

ART-CranberryJuice-11-23-2011

Binary PackagesLinuxMacOS XWindows64-bit system 32-bit system Source PackagesART 454 read simulator ART Illumina read simulator ART SOLiD read simulator

ART-ApplePie-04-21-2011

Binary PackagesLinuxMacOS XWindows64-bit system 32-bit system Source PackagesART 454 read simulator ART Illumina read simulator ART SOLiD read simulator

Installation

Compilation and installation from a source packageCompilation 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 installInstallation from a binary packageInstallation 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.gzART 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 simulationSingle-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 20Paired-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 20Illumina read simulationSingle-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_endPaired-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_endMate-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_endSOLiD read simulationSingle-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 10Paired-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