SOAP3-dp：快速、准确、灵敏的基于GPU的短读对齐器
SOAP3-dp: Fast, Accurate and Sensitive GPU-based Short Read Aligner
摘要：
为了解决下一代测序（NGS）的指数级增加的通量，大多数现有的短读段比对器可以被配置为在准确性和灵敏度的交易中有利于速度。SOAP 3-dp通过利用CPU和GPU的计算能力以及优化的算法，同时提供高速度和灵敏度。与广泛采用的比对器（包括BWA、Bowtie 2、SeqAlto、GEM）和基于GPU的比对器（包括BarraCUDA和EQUIPHAW）相比，SOAP 3-dp的速度快2到10倍，同时在不同长度的Illumina读取上保持最高的灵敏度和最低的错误发现率（FDR）。超越了它的前身SOAP 3，它不允许间隙对齐，SOAP 3-dp默认容忍对齐相似性低至60%。使用人类基因组的真实数据评估表明SOAP 3-dp能够发现更真实的变体和更长的Indel。Fosmid测序显示新发现的缺失的FDR为9.1%。SOAP 3-dp本身支持BAM文件格式，并提供与BWA相同的评分方案，这使其能够集成到现有的分析管道中。SOAP 3-dp已在Amazon-EC 2、NIH-Biowulf和天河-1A上部署。
英文摘要：
To tackle the exponentially increasing throughput of Next-Generation Sequencing (NGS), most of the existing short-read aligners can be configured to favor speed in trade of accuracy and sensitivity. SOAP3-dp, through leveraging the computational power of both CPU and GPU with optimized algorithms, delivers high speed and sensitivity simultaneously. Compared with widely adopted aligners including BWA, Bowtie2, SeqAlto, GEM and GPU-based aligners including BarraCUDA and CUSHAW, SOAP3-dp is two to tens of times faster, while maintaining the highest sensitivity and lowest false discovery rate (FDR) on Illumina reads with different lengths. Transcending its predecessor SOAP3, which does not allow gapped alignment, SOAP3-dp by default tolerates alignment similarity as low as 60 percent. Real data evaluation using human genome demonstrates SOAP3-dp's power to enable more authentic variants and longer Indels to be discovered. Fosmid sequencing shows a 9.1 percent FDR on newly discovered deletions. SOAP3-dp natively supports BAM file format and provides a scoring scheme same as BWA, which enables it to be integrated into existing analysis pipelines. SOAP3-dp has been deployed on Amazon-EC2, NIH-Biowulf and Tianhe-1A.
机构、总结、中文摘要均由AI分析而来，可能存在错误，请以论文正文为准。
