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PMID: 21897427 Published · epublish English Journal Article Research Support, U.S. Gov't, Non-P.H.S. Review

Next-generation transcriptome assembly.

Nature reviews. Genetics ·Vol. 12 ·No. 10 ·2011-09-07 ·Pages 671-82

Martin JA, Wang Z

Abstract

Transcriptomics studies often rely on partial reference transcriptomes that fail to capture the full catalogue of transcripts and their variations. Recent advances in sequencing technologies and assembly algorithms have facilitated the reconstruction of the entire transcriptome by deep RNA sequencing (RNA-seq), even without a reference genome. However, transcriptome assembly from billions of RNA-seq reads, which are often very short, poses a significant informatics challenge. This Review summarizes the recent developments in transcriptome assembly approaches - reference-based, de novo and combined strategies - along with some perspectives on transcriptome assembly in the near future.

MeSH Terms
Animals Base Sequence Cloning, Molecular Gene Expression Profiling/methods,trends Gene Library Humans Models, Biological Molecular Sequence Annotation/methods,trends Molecular Sequence Data Sequence Analysis, DNA/methods,trends Sequence Analysis, RNA/methods,trends
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Martin Jeffrey A
Lawrence Berkeley National Laboratory, DOE Joint Genome Institute, 2800 Mitchell Drive, MS100 Walnut Creek, California 94598, USA. [email protected]
Wang Zhong
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Article Info
Journal
Nature reviews. Genetics
Abbr.
Nat Rev Genet
ISSN
1471-0064
DOI
10.1038/nrg3068
Email
[email protected]
Published
2011-09-07
Epub
2011-00-07
Pages
671-82
Language
English
Region
England
NLM ID
100962779
Subset
IM
External Links
PubMed source DOI: 10.1038/nrg3068 View journal details
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