期刊
JOURNAL OF BIOTECHNOLOGY
卷 261, 期 -, 页码 157-168出版社
ELSEVIER SCIENCE BV
DOI: 10.1016/j.jbiotec.2017.07.017
关键词
NGS analysis; Software libraries; C plus; Data structures
资金
- Intel Parallel Compute Center at FU Berlin
- German Science Foundation (DFG) [RE 1712/4-1, RE 1712/3-1, RE 1712/3-2]
- German Federal Ministry of Education and Research (BMBF) [031A535B]
- Max Planck society
Background: The use of novel algorithmic techniques is pivotal to many important problems in life science. For example the sequencing of the human genome (Venter et al., 2001) would not have been possible without advanced assembly algorithms and the development of practical BWT based read mappers have been instrumental for NGS analysis. However, owing to the high speed of technological progress and the urgent need for bioinformatics tools, there was a widening gap between state-of-the-art algorithmic techniques and the actual algorithmic components of tools that are in widespread use. We previously addressed this by introducing the SeqAn library of efficient data types and algorithms in 2008 ( Doring et al., 2008). Results: The SeqAn library has matured considerably since its first publication 9 years ago. In this article we review its status as an established resource for programmers in the field of sequence analysis and its contributions to many analysis tools. Conclusions: We anticipate that SeqAn will continue to be a valuable resource, especially since it started to actively support various hardware acceleration techniques in a systematic manner.
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