De novo assembly of transcriptome from next-generation sequencing data

Li, Xuan, Kong, Yimeng, Zhao, Qiong-Yi, Li, Yuan-Yuan and Hao, Pei (2016) De novo assembly of transcriptome from next-generation sequencing data. Quantitative Biology, 4 2: 94-105. doi:10.1007/s40484-016-0069-y


Author Li, Xuan
Kong, Yimeng
Zhao, Qiong-Yi
Li, Yuan-Yuan
Hao, Pei
Title De novo assembly of transcriptome from next-generation sequencing data
Formatted title
De novo assembly of transcriptome from next-generation sequencing data
Journal name Quantitative Biology   Check publisher's open access policy
ISSN 2095-4697
2095-4689
Publication date 2016-06-01
Sub-type Article (original research)
DOI 10.1007/s40484-016-0069-y
Open Access Status Not yet assessed
Volume 4
Issue 2
Start page 94
End page 105
Total pages 12
Place of publication Heidelberg, Germany
Publisher Springer
Collection year 2017
Language eng
Formatted abstract
Reconstruction of transcriptome by de novo assembly from next generation sequencing (NGS) short-sequence reads provides an essential mean to catalog expressed genes, identify splicing isoforms, and capture the expression detail of transcripts for organisms with no reference genome available. De novo transcriptome assembly faces many unique challenges, including alternative splicing, variable expression level covering a dynamic range of several orders of magnitude, artifacts introduced by reverse transcription, etc. In the current review, we illustrate the grand strategy in applying De Bruijn Graph (DBG) approach in de novo transcriptome assembly.We further analyze many parameters proven critical in transcriptome assembly using DBG. Among them, k-mer length, coverage depth of reads, genome complexity, performance of different programs are addressed in greater details. A multi-k-mer strategy balancing efficiency and sensitivity is discussed and highly recommended for de novo transcriptome assembly. Future direction points to the combination of NGS and third generation sequencing technology that would greatly enhance the power of de novo transcriptomics study.
Keyword Transcriptome
De novo assembly
De Bruijn Graph
Next generation sequencing
K-mer length
RNA splicing
Performance
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: HERDC Pre-Audit
Queensland Brain Institute Publications
 
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Created: Tue, 27 Sep 2016, 21:40:21 EST by Kirstie Asmussen on behalf of School of Music