Vyverman Michaël, Baets Bernard De, Fack Veerle, Dawyndt Peter
Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Krijgslaan 281 Building S9, Ghent, B-9000, Belgium.
Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Coupure links 653, Ghent, B-9000, Belgium.
BMC Bioinformatics. 2015 May 15;16(1):159. doi: 10.1186/s12859-015-0533-0.
Rapid evolutions in sequencing technology force read mappers into flexible adaptation to longer reads, changing error models, memory barriers and novel applications.
ALFALFA achieves a high performance in accurately mapping long single-end and paired-end reads to gigabase-scale reference genomes, while remaining competitive for mapping shorter reads. Its seed-and-extend workflow is underpinned by fast retrieval of super-maximal exact matches from an enhanced sparse suffix array, with flexible parameter tuning to balance performance, memory footprint and accuracy.
ALFALFA is open source and available at http://alfalfa.ugent.be .
测序技术的快速发展迫使读段比对工具灵活适应更长的读段、不断变化的错误模型、内存限制和新应用。
ALFALFA在将长单端和双端读段准确比对到千兆碱基规模的参考基因组方面表现出高性能，同时在比对较短读段时也具有竞争力。其种子扩展工作流程基于从增强的稀疏后缀数组中快速检索超最大精确匹配，并通过灵活的参数调整来平衡性能、内存占用和准确性。
ALFALFA是开源的，可从http://alfalfa.ugent.be获取。
