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Genome Annotation and Assembly

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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.

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Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...

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Protocol for transcriptome assembly by the TransBorrow algorithm.

Dengyi Zhao¹, Juntao Liu¹, Ting Yu²

¹School of Mathematics and Statistics, Shandong University, Weihai 264209, China.

Biology Methods & Protocols

|November 29, 2023

Summary

This summary is machine-generated.

TransBorrow is a new software for assembling short RNA-seq reads into full-length transcripts. This tool aids in transcriptome analysis by providing fast and accurate transcript assembly and expression quantification.

Keywords:

RNA-seq data splice variants transcriptome assembly

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Area of Science:

Genomics
Bioinformatics
Molecular Biology

Background:

High-throughput RNA sequencing (RNA-seq) generates vast amounts of data for transcriptome analysis.
Short read lengths from RNA-seq pose challenges for accurate full-length transcript assembly.
Efficient tools are crucial for assembling and quantifying transcript expression from short reads.

Purpose of the Study:

To introduce TransBorrow, a novel software tool for transcriptome assembly.
To provide a protocol for utilizing TransBorrow with short RNA-seq reads.
To enable fast, accurate, and flexible analysis of transcriptomes from short-read data.

Main Methods:

Developed TransBorrow, a transcriptome assembly software optimized for short reads.
Integrated TransBorrow with splice-aware alignment tools (e.g., Hisat2, Star).
Combined TransBorrow with existing transcriptome assemblers (e.g., StringTie, Cufflinks, Scallop).
Detailed a comprehensive protocol from raw data processing to expression quantification.

Main Results:

TransBorrow facilitates the assembly of full-length transcripts from short RNA-seq reads.
The protocol enables accurate quantification of expressed transcript abundances.
The method is designed for speed and flexibility across different computational platforms.

Conclusions:

TransBorrow offers an effective solution for transcriptome assembly using short RNA-seq reads.
The protocol provides a complete workflow for analyzing short-read RNA-seq data.
This approach enhances the utility of high-throughput sequencing for transcriptomic studies.