About ART

ART is a set of efficient simulators for generating synthetic sequence read data of next-generation sequencers including Illumina, 454 and SOLiD machines. The tool is useful for assessing results and performance of computational methods and software tools for ChIP-seq data analysis, polymorphism discovery and genome assembly. ART was used as a primary tool for the simulation study of the 1000 Genomes Project.

Features

Support Illumina, 454, and SOLiD sequence read simulation
Support base substitutions, insertions and deletions
Capable of generating single-end and paired-end reads
Use position dependent error profile or empirical quality score distributions
Base call error (substitution) is straightly correlated with base quality scores
Allow scalable error rate or profile
Efficiently implemented in C++ with optimized algorithms
Support multiple OS platforms including Linux, Windows and MacOS

Availability

ART is freely available to the public.

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Usage

============================================================================= ART FOR 454 READ SIMULATION ============================================================================= USAGE: ART_454 INPUT_SEQ_FILE OUTPUT_FILE_PREFIX FOLD_COVERAGE ART_454 INPUT_SEQ_FILE OUTPUT_FILE_PREFIX FOLD_COVERAGE MEAN_FLAG_LEN STD_DEV EXAMPLES: ART_454 ref_genome.fa ./outdir/out_file 20 ART_454 ref_genome.fa ./outdir/out_file 20 1000 20 ============================================================================= ART FOR ILLUMINA READ SIMULATION ============================================================================= X version: sequence read quality is based on Illumina read error profile USAGE: ART INPUT_SEQ_FILE OUTPUT_FILE_PREFIX LEN_READ FOLD_COVERAGE ART INPUT_SEQ_FILE OUTPUT_FILE_PREFIX LEN_READ FOLD_COVERAGE MEAN_FLAG_LEN STD_DEV ART INPUT_SEQ_FILE OUTPUT_FILE_PREFIX LEN_READ FOLD_COVERAGE ERROR_SCALE_FACTOR ART INPUT_SEQ_FILE OUTPUT_FILE_PREFIX LEN_READ FOLD_COVERAGE MEAN_FLAG_LEN STD_DEV ERROR_SCALE_FACTOR EXAMPLES: art ref_geneome.fa out_seq_read 32 10 art ref_geneome.fa out_seq_read 32 10 200 20 art ref_geneome.fa out_seq_read 32 10 1.2 art ref_geneome.fa out_seq_read 32 10 200 20 1.2 Q version: sequence read quality is based on empirical distribution of quality scores USAGE: ART INPUT_SEQ_FILE OUTPUT_FILE_PREFIX LEN_READ FOLD_COVERAGE [ID] ART INPUT_SEQ_FILE OUTPUT_FILE_PREFIX LEN_READ FOLD_COVERAGE MEAN_FLAG_LEN STD_DEV [ID] EXAMPLES: art reference_DNA.fa outfile_prefix 32 10 art reference_DNA.fa outfile_prefix 32 10 300 30 ============================================================================= ART FOR SOLiD READ SIMULATION ============================================================================= USAGE: ART INPUT_SEQ_FILE OUTPUT_FILE_PREFIX LEN_READ FOLD_COVERAGE ART INPUT_SEQ_FILE OUTPUT_FILE_PREFIX LEN_READ FOLD_COVERAGE MEAN_FLAG_LEN STD_DEV EXAMPLES: art ref_geneome.fa out_seq_read 32 10 art ref_geneome.fa out_seq_read 32 10 200 20

Input parameters:

INPUT_SEQ_FILE: DNA sequence in FASTA format
OUTPUT_FILE_PREFIX: Common prefix of output file names
LEN_READ: the length of read
FOLD_COVERAGE: fold of read coverage
MEAN_FLAG_LEN: mean fragment size of paired-end reads
STD_DEV: standard deviation of paired-end read fragment sizes

Output files:

*.fa files: sequence reads in FASTA format
*.qual files: quality scores in FASTA format
*.aln: read alignments to the genome

Datasets

Simulation datasets for the 1000 Genomes Project

Authors

Weichun Huang in collaboration with Gabor Marth