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Pharmaceutics 2015, 7(4), 523-541; doi:10.3390/pharmaceutics7040523

Alignment of Short Reads: A Crucial Step for Application of Next-Generation Sequencing Data in Precision Medicine

Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA
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Academic Editor: Afzal R. Mohammed
Received: 21 October 2015 / Revised: 14 November 2015 / Accepted: 17 November 2015 / Published: 23 November 2015
(This article belongs to the Special Issue Personalized Medicine and Pharmacogenomics)
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Abstract

Precision medicine or personalized medicine has been proposed as a modernized and promising medical strategy. Genetic variants of patients are the key information for implementation of precision medicine. Next-generation sequencing (NGS) is an emerging technology for deciphering genetic variants. Alignment of raw reads to a reference genome is one of the key steps in NGS data analysis. Many algorithms have been developed for alignment of short read sequences since 2008. Users have to make a decision on which alignment algorithm to use in their studies. Selection of the right alignment algorithm determines not only the alignment algorithm but also the set of suitable parameters to be used by the algorithm. Understanding these algorithms helps in selecting the appropriate alignment algorithm for different applications in precision medicine. Here, we review current available algorithms and their major strategies such as seed-and-extend and q-gram filter. We also discuss the challenges in current alignment algorithms, including alignment in multiple repeated regions, long reads alignment and alignment facilitated with known genetic variants. View Full-Text
Keywords: precision medicine; next-generation sequencing; genetic variants; alignment; short reads precision medicine; next-generation sequencing; genetic variants; alignment; short reads
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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MDPI and ACS Style

Ye, H.; Meehan, J.; Tong, W.; Hong, H. Alignment of Short Reads: A Crucial Step for Application of Next-Generation Sequencing Data in Precision Medicine. Pharmaceutics 2015, 7, 523-541.

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