Abstract
Present-day high-throughput sequencing techniques routinely produce a flood of genomic information (as high as 540-600 Gbases/machine/week for some technologies). The output comes under the form of short sequence reads; in a typical resequencing application (where the knowledge of a reference genome for the organism being studied is assumed) the sequence reads need to be aligned to the reference.
Such high yields make the use of traditional alignment programs like BLAST unpractical; while resequencing, on the other hand, one is usually interested in considering only matches showing a very high sequence similarity with the original read. This new working setup required the development of a generation of new high-throughput lower-sensitivity alignment programs, called short-read mappers.
Influenced by the standpoint of the algorithm designer, published literature tends to overemphasize speed, and standard working conditions, at the expense of accuracy. In this chapter we attempt to review the state-of-the-art of short-read alignment technology, focusing more on the user’s standpoint, and on what is necessary to know to be able to design a high-quality mapping analysis workflow, rather than on purely technical issues.
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Ribeca, P. (2012). Short-Read Mapping. In: Rodríguez-Ezpeleta, N., Hackenberg, M., Aransay, A. (eds) Bioinformatics for High Throughput Sequencing. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-0782-9_7
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