Computational Biology
Computational biology is an interdisciplinary field that applies mathematical, statistical, and computer science methods to answer biological questions, and its importance has only increased with the introduction of high-throughput techniques such as auto
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1. Introduction Recent advances in sequencing technologies have resulted in a dramatic reduction of sequencing costs and a corresponding increase in throughput. As data produced by these technologies is rapidly becoming available, it is increasingly clear that software tools developed for the assembly and analysis of Sanger data are ill-suited to handle the specific characteristics of new generation sequencing data. In particular, these technologies generate much shorter read lengths (as low as 35 bp), complicating repeat resolution during both de novo assembly and while mapping the reads to a reference genome. Furthermore, the sheer size of the data produced by the new sequencing machines poses performance problems not previously encountered in Sanger data. This is further exacerbated by the fact that the new technologies make it possible for individual labs (rather than large sequencing centers) to perform high-throughput sequencing experiments, and these labs do not have the computational infrastructure commonly David Fenyö (ed.), Computational Biology, Methods in Molecular Biology, vol. 673, DOI 10.1007/978-1-60761-842-3_1, © Springer Science+Business Media, LLC 2010
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Nagarajan and Pop
available at large sequencing facilities. In this paper we survey software packages recently developed to specifically handle new generation sequencing data. We briefly overview the main characteristics of the new sequencing technologies and the computational challenges encountered in the assembly of such data; however, a full survey of these topics is beyond the scope of our paper. For more information, we refer the reader to other surveys on sequencing and assembly (1–3). We hope the information provided here will provide a starting point for any researcher interested in applying the new technologies to either de novo sequencing applications or to resequencing projects. Due to the rapid pace of technological and software developments in this field we try to focus on more general concepts and urge the reader to follow the links provided in order to obtain up-to-date information about the software packages described.
2. Sequencing Technologies Before discussing the software tools available for analyzing the new generation sequencing data we briefly summarize the specific characteristics of these technologies. For a more in-depth summary, the reader is referred to a recent review by Mardis (1). 2.1. Roche/454 Pyrosequencing
The first, and arguably most mature, of the new generation sequencing technologies is the pyrosequencing approach from Roche/454 Life Sciences. Current sequencing instruments (GS FLX Titanium) can generate in a single run ~500 Mbp of DNA in sequencing reads that are ~400 bp in length (approximately 1.2 million reads per run), while the previous generation instruments (GS FLX) generate ~100 Mbp of DNA in reads that are ~250 bp in length (approximately 400,000 reads per run). Initial versions of mate-pair protocols are also available that generate paired reads spaced by approximately 3 kbp. The main ch
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