Mathematics

Dynamic programming

Wireless

Operating system

Algorithm

Statistics

Engineering

Parallel computing

Throughput

Programming language

Sensitivity (control systems)

Electronic engineering

Index (typography)

Software

Computer science

Flexibility (engineering)

Computer hardware

Nature Methods

The Bowtie 2 software achieves fast, sensitive, accurate and memory-efficient gapped alignment of sequencing reads using the full-text minute index and hardware-accelerated dynamic programming algorithms. As the rate of sequencing increases, greater throughput is demanded from read aligners. The full-text minute index is often used to make alignment very fast and memory-efficient, but the approach is ill-suited to finding longer, gapped alignments. Bowtie 2 combines the strengths of the full-text minute index with the flexibility and speed of hardware-accelerated dynamic programming algorithms to achieve a combination of high speed, sensitivity and accuracy.

Fast gapped-read alignment with Bowtie 2