2013, Vol. 41, No. 10 | Yang Liao, Gordon K. Smyth, Wei Shi
The article introduces a new multi-seed alignment strategy called "seed-and-vote" for mapping reads to a reference genome. This method uses a large number of short, equi-spaced seeds (subreads) extracted from each read and allows all subreads to vote on the optimal genomic location for the read. The strategy is designed to be fast, sensitive, and accurate, with the overall genomic location chosen before detailed alignment. It scales well for longer reads and can be extended to detect exon junctions in RNA-seq data. The authors compare the performance of their method with other popular aligners using extensive test scenarios, including simulations and real data sets from the 1000 Genomes project and the Sequencing Quality Control (SEQC) project. The results show that the seed-and-vote method is competitive in terms of sensitivity, accuracy, and speed.The article introduces a new multi-seed alignment strategy called "seed-and-vote" for mapping reads to a reference genome. This method uses a large number of short, equi-spaced seeds (subreads) extracted from each read and allows all subreads to vote on the optimal genomic location for the read. The strategy is designed to be fast, sensitive, and accurate, with the overall genomic location chosen before detailed alignment. It scales well for longer reads and can be extended to detect exon junctions in RNA-seq data. The authors compare the performance of their method with other popular aligners using extensive test scenarios, including simulations and real data sets from the 1000 Genomes project and the Sequencing Quality Control (SEQC) project. The results show that the seed-and-vote method is competitive in terms of sensitivity, accuracy, and speed.