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Updated: Apr 13, 2026

Targeted DNA Methylation Analysis by Next-generation Sequencing
Published on: February 24, 2015
Alignment of Next-Generation Sequencing Reads
Knut Reinert1, Ben Langmead, David Weese
1Department of Mathematics and Computer Science, Freie Universität Berlin, 14195 Berlin, Germany; email: knut.reinert@fu-berlin.de , david.weese@fu-berlin.de.
Abstract:
High-throughput DNA sequencing has considerably changed the possibilities for conducting biomedical research by measuring billions of short DNA or RNA fragments. A central computational problem, and for many applications a first step, consists of determining where the fragments came from in the original genome. In this article, we review the main techniques for generating the fragments, the main applications, and the main algorithmic ideas for computing a solution to the read alignment problem. In addition, we describe pitfalls and difficulties connected to determining the correct positions of reads.
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