Fast and Accurate Read Alignment for Resequencing

Department of Electrical Engineering, Stanford University, Stanford, CA 94305, USA, Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA, Bina Technologies Inc., Redwood City and Department of Statistics, Stanford University, Stanford, CA 94305, USA.
Bioinformatics (Impact Factor: 4.98). 07/2012; 28(18):2366-73. DOI: 10.1093/bioinformatics/bts450
Source: PubMed


Next-generation sequence analysis has become an important task both in laboratory and clinical settings. A key stage in the majority sequence analysis workflows, such as resequencing, is the alignment of genomic reads to a reference genome. The accurate alignment of reads with large indels is a computationally challenging task for researchers.
We introduce SeqAlto as a new algorithm for read alignment. For reads longer than or equal to 100 bp, SeqAlto is up to 10 × faster than existing algorithms, while retaining high accuracy and the ability to align reads with large (up to 50 bp) indels. This improvement in efficiency is particularly important in the analysis of future sequencing data where the number of reads approaches many billions. Furthermore, SeqAlto uses less than 8 GB of memory to align against the human genome. SeqAlto is benchmarked against several existing tools with both real and simulated data.
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Available from: John Chong Mu
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    • "Lately, the SOAP3 research team released SOAP3-dp, a new version of the aligner that exploits dynamic programming to support gapped alignments. Compared with BWA, Bowtie2 [52], SeqAlto [53], GEM [54], and the previously mentioned GPU-based aligners, SOAP3-dp is two to tens of times faster, while maintaining the highest sensitivity and lowest false discovery rate on Illumina reads with different lengths. Table 1 summarizes the described tools. "
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    ABSTRACT: 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, CUSHAW2, GEM and GPU-based aligners BarraCUDA and CUSHAW, SOAP3-dp was found to be 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%. 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% FDR on newly discovered deletions. SOAP3-dp natively supports BAM file format and provides the same scoring scheme 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.
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