WHAM: A High-Throughput Sequence Alignment Method

• Autores: Yinan Li, Jignesh M. Patel, Allison Terrell
• Localización: ACM transactions on database systems, ISSN 0362-5915, Vol. 37, Nº 4, 2012
• Idioma: inglés
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• Resumen

  • Over the last decade, the cost of producing genomic sequences has dropped dramatically due to the current so-called next-generation sequencing methods. However, these next-generation sequencing methods are critically dependent on fast and sophisticated data processing methods for aligning a set of query sequences to a reference genome using rich string matching models. The focus of this work is on the design, development and evaluation of a data processing system for this crucial “short read alignment” problem. Our system, called WHAM, employs hash-based indexing methods and bitwise operations for sequence alignments. It allows rich match models and it is significantly faster than the existing state-of-the-art methods. In addition, its relative speedup over the existing method is poised to increase in the future in which read sequence lengths will increase.