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From Sequence Mapping to Genome Assemblies

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Parasite Genomics Protocols

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1201))

Abstract

The development of “next-generation” high-throughput sequencing technologies has made it possible for many labs to undertake sequencing-based research projects that were unthinkable just a few years ago. Although the scientific applications are diverse, e.g., new genome projects, gene expression analysis, genome-wide functional screens, or epigenetics—the sequence data are usually processed in one of two ways: sequence reads are either mapped to an existing reference sequence, or they are built into a new sequence (“de novo assembly”). In this chapter, we first discuss some limitations of the mapping process and how these may be overcome through local sequence assembly. We then introduce the concept of de novo assembly and describe essential assembly improvement procedures such as scaffolding, contig ordering, gap closure, error evaluation, gene annotation transfer and ab initio gene annotation. The results are high-quality draft assemblies that will facilitate informative downstream analyses.

An erratum to this chapter is available at http://dx.doi.org/10.1007/978-1-4939-1438-8_21

An erratum to this chapter can be found at http://dx.doi.org/10.1007/978-1-4939-1438-8_21

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Acknowledgements

I would like to thank Adam Reid, Martin Hunt, and Bernardo Foth for proofreading the chapter.

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Correspondence to Thomas D. Otto .

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Otto, T.D. (2015). From Sequence Mapping to Genome Assemblies. In: Peacock, C. (eds) Parasite Genomics Protocols. Methods in Molecular Biology, vol 1201. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-1438-8_2

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  • DOI: https://doi.org/10.1007/978-1-4939-1438-8_2

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-1437-1

  • Online ISBN: 978-1-4939-1438-8

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