ART: a next-generation sequencing read simulator

By Weichun Huang, Leping Li, Jason R. Myers, Gabor T. Marth. Bioinform., 2012

1,471 citations recorded by the source corpus.

Subfields: Cancer Research, Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/cdb91f039a0e7f5fde482d930f2acab358758691

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Cancer Research

In Genetics

In Molecular Biology

Citations in the corpus

Comprehensive evaluation of structural variation detection algorithms for whole genome sequencing (2019, positive): “A variety of read sets of Sim-A with different statics in read length (100 bp, 125 bp, and 150 bp), insert size (400 bp, 500 bp, and 600 bp), and coverage (10×, 20×, 30×, and 60×) were generated with the simulated paternal and maternal genomes of Sim-A using the ART simulator [78].”
Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads (2016, neutral): “8) to generate six synthetic paired-end short-read sets from each reference genome which mimic those from an Illumina HiSeq 2500: 125 bp read length, 400 bp mean insert size, 60 bp insert size standard deviation and 50x read depth[40,41].”
Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads (2014, positive): “General information We simulated 10 million 100 bp + 100 bp PE Solexa reads from the Arabidopsis thaliana genome using ART, a NGS read simulator [15], with some revision on the source codes for simulating adapter-contaminated reads (http://sourceforge.”
Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns (2017, positive): “Reads were simulated from this real community using ART (12) to produce Illumina-like sequence data.”
The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote (2013, neutral): “Versions of Mason and Art used are 0.1 and 1.5.0, respectively.”
Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3 (2020, positive): “We constructed additional synthetic metagenomes by sampling sequencing reads from curated microbial genome sets using ART (Huang et al., 2012) with an Illumina HiSeq 2500 error model.”
Polypolish: Short-read polishing of long-read bacterial genome assemblies (2021, positive): “Paired-end short reads were simulated with ART v2016–06-05 [23] using the following parameters: 100 × depth, HiSeqX TruSeq preset, 150 bp read length, 400 bp mean fragment length, 50 bp fragment length standard deviation, and all other parameters left at defaults.”