art_modern: An Accelerated ART Simulator of Diverse Next-Generation Sequencing Reads

Abstract

SummaryFast simulation of next-generation sequencing (NGS) data is vital for software development and benchmarking. Here we describe art_modern, an accelerated ART simulator that can simulate various NGS data. We accelerated ART using updated sampling algorithms, single-instruction multiple-data (SIMD) instruction-set extensions (ISEs), thread- and node-level parallelism, and an asynchronous output writer, while enabling simulation of transcriptome profiling data by supporting contig-specific coverage with strand information. The new implementation was benchmarked against popular performance-oriented NGS simulators, revealing a 75-77% reduction in CPU time and a 15-24 times acceleration in wall-clock time on a multi-core machine compared to the original implementation. With this simulator, the process of developing and benchmarking NGS sequence analysis algorithms can be largely accelerated. Availability and ImplementationThe software is implemented in C++17 with CMake as the building system. It can be built and executed on a modern GNU/Linux operating system with Boost, Zlib, and a C++17 compiler, with further acceleration available using Intel OneAPI C++/DPC++ compilers and Intel oneAPI MKL random generators. The software is available at https://github.com/YU-Zhejian/art_modern under the GNU General Public License v3. ContactZhejian Yu (yuzj25@seas.upenn.edu)