Tool: Art: Simulation Tools To Generate Synthetic Next-Generation Sequencing Reads.
gravatar for Istvan Albert
8.2 years ago by
Istvan Albert ♦♦ 84k
University Park, USA
Istvan Albert ♦♦ 84k wrote:

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.

sequence tool • 11k views
ADD COMMENTlink modified 5.5 years ago by geek_y11k • written 8.2 years ago by Istvan Albert ♦♦ 84k

I'm interested in using ART to simulate Illumina reads at 300bp lengths. This doesn't seem immediately possible given the provided quality profiles. Any idea if it is possible to use ART to simulate 300bp Illumina reads or should I look towards another application?

ADD REPLYlink written 5.0 years ago by Jonathan King0

To answer my earlier question, it is possible to simulate Illumina reads at longer lengths provided you generate the error profiles with ART using input files that have the desired length.

ADD REPLYlink written 4.2 years ago by Jonathan King0

I am able to synthetic generate reads by ART but i am unable to increase or decrease the error rate in the reads. My question is can we alter the error rate of the synthesis reads using ART. IF yes then how.?

ADD REPLYlink written 5.0 years ago by kshitijtayal40
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