fast gapped read alignment with bowtie 2

#Fast gapped read alignment with bowtie 2 software#

PLoS Comput Biol 16(11):Įditor: Manja Marz, bioinformatics, GERMANY As WGS data accumulates exponentially and high-concurrency computational resources become widespread, Arioc addresses a growing need for timely computation in the short-read data analysis toolchain.Ĭitation: Wilton R, Szalay AS (2020) Arioc: High-concurrency short-read alignment on multiple GPUs. With this additional acceleration, Arioc computes two million short-read alignments per second in a four-GPU system it can align the reads from a human WGS sequencer run–over 500 million 150nt paired-end reads–in less than 15 minutes. By modifying Arioc's implementation to exploit this GPU memory architecture we obtained a further 1.8x-2.9x increase in overall alignment speeds. We have adapted Arioc to recent multi-GPU hardware architectures that support high-bandwidth peer-to-peer memory accesses among multiple GPUs.

#Fast gapped read alignment with bowtie 2 software#

When two or more GPUs are available, Arioc's speed increases proportionately because the software executes concurrently on each available GPU device.

Arioc, a GPU-accelerated short-read aligner, can compute WGS (whole-genome sequencing) alignments ten times faster than comparable CPU-only alignment software. This presents an opportunity for DNA sequence alignment software to exploit high-concurrency hardware to generate short-read alignments at high speed. In large DNA sequence repositories, archival data storage is often coupled with computers that provide 40 or more CPU threads and multiple GPU (general-purpose graphics processing unit) devices.