Related Experiment Video
Updated: May 8, 2026
12:08
Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies
Published on: August 20, 2021
Augmenting transcriptome assembly by combining de novo and genome-guided tools.
Prachi Jain1, Neeraja M Krishnan1, Binay Panda1,2
1Ganit Labs, Bio-IT Centre, Institute of Bioinformatics and Applied Biotechnology, Bangalore, India.
Peerj
|September 12, 2013
Summary
Choosing transcriptome assembly tools is challenging. Combining de novo and genome-guided approaches, specifically Trinity and TopHat1-Cufflinks, improves transcript recovery and full-length transcript identification for non-model species.
Area of Science:
- Bioinformatics
- Computational Biology
- Genomics
Background:
- Transcriptome assembly is crucial for understanding gene expression, especially in non-model organisms.
- Current de novo and genome-guided assemblers have limitations in sensitivity, specificity, and full-length transcript recovery.
Purpose of the Study:
- To comprehensively compare the performance of various de novo and genome-guided transcriptome assemblers.
- To introduce and evaluate a combinatorial approach augmenting assembly using both types of tools.
Main Methods:
- Comparative analysis of multiple de novo and genome-guided transcriptome assembly tools.
- Development and testing of a hybrid assembly strategy combining outputs from different assemblers.
Main Results:
- Trinity demonstrated the best overall transcript recovery.
- TopHat1-Cufflinks yielded the highest number of full-length transcripts.
- Augmenting Trinity with TopHat1-Cufflinks significantly improved sensitivity and isoform recovery without substantial loss of specificity.
Conclusions:
- No single assembler is optimal for all transcriptome assembly tasks.
- A combinatorial approach using both de novo and genome-guided assemblers enhances the quality of transcriptome reconstruction.
- The proposed hybrid method offers a superior strategy for obtaining comprehensive and accurate transcriptomes, particularly for non-model species.
Related Concept Videos
03:36Genome Annotation and Assembly
The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
03:21RNA-seq
RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...