Department of Computer Science, The University of Hong Kong, Hong Kong, China.
Bioinformatics. 2012 Mar 15;28(6):878-9. doi: 10.1093/bioinformatics/bts061. Epub 2012 Jan 28.
SOAP3 is the first short read alignment tool that leverages the multi-processors in a graphic processing unit (GPU) to achieve a drastic improvement in speed. We adapted the compressed full-text index (BWT) used by SOAP2 in view of the advantages and disadvantages of GPU. When tested with millions of Illumina Hiseq 2000 length-100 bp reads, SOAP3 takes < 30 s to align a million read pairs onto the human reference genome and is at least 7.5 and 20 times faster than BWA and Bowtie, respectively. For aligning reads with up to four mismatches, SOAP3 aligns slightly more reads than BWA and Bowtie; this is because SOAP3, unlike BWA and Bowtie, is not heuristic-based and always reports all answers.
SOAP3 是第一个利用图形处理单元（GPU）中的多处理器来实现速度大幅提升的短读对齐工具。我们针对 GPU 的优缺点，对 SOAP2 中使用的压缩全文索引（BWT）进行了调整。在使用数百万个 Illumina Hiseq 2000 长度为 100bp 的读取进行测试时，SOAP3 在将 100 万个读取对映射到人类参考基因组上时，所需时间不到 30 秒，与 BWA 和 Bowtie 相比，速度分别至少快 7.5 倍和 20 倍。对于最多允许四个错配的读取对齐，SOAP3 比 BWA 和 Bowtie 对齐的读取略多一些；这是因为 SOAP3 与 BWA 和 Bowtie 不同，它不是基于启发式的，并且总是报告所有答案。
