@article{li2012wham,
author = {Li, Yinan and Patel, Jignesh M. and Terrell, Allison},
title = {WHAM: A High-Throughput Sequence Alignment Method},
year = {2012},
month = {December},
abstract = {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.},
url = {http://approjects.co.za/?big=en-us/research/publication/wham-a-high-throughput-sequence-alignment-method/},
pages = {28},
journal = {ACM Trans. Database Syst.},
volume = {37},
edition = {ACM Trans. Database Syst.},
number = {4},
}