A simple guide to de novo transcriptome assembly and annotation

Abstract A transcriptome constructed from short-read RNA sequencing (RNA-seq) is an easily attainable proxy catalog of protein-coding genes when genome assembly is unnecessary, expensive or difficult. In the absence of a sequenced genome to guide the reconstruction process, the transcriptome must be...

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Bibliographic Details
Published inBriefings in bioinformatics Vol. 23; no. 2
Main Authors Raghavan, Venket, Kraft, Louis, Mesny, Fantin, Rigerte, Linda
Format Journal Article
LanguageEnglish
Published England Oxford University Press 10.03.2022
Oxford Publishing Limited (England)
Subjects
Annotations
Assembly
Gene sequencing
Genome
Genomes
High-Throughput Nucleotide Sequencing
Molecular Sequence Annotation
Proteins
Review
Ribonucleic acid
RNA
Sequence Analysis, RNA - methods
Transcriptome
Transcriptomes
Workflow
annotation
assembly
RNA-seq
tools
de novo
transcriptome
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Summary:Abstract A transcriptome constructed from short-read RNA sequencing (RNA-seq) is an easily attainable proxy catalog of protein-coding genes when genome assembly is unnecessary, expensive or difficult. In the absence of a sequenced genome to guide the reconstruction process, the transcriptome must be assembled de novo using only the information available in the RNA-seq reads. Subsequently, the sequences must be annotated in order to identify sequence-intrinsic and evolutionary features in them (for example, protein-coding regions). Although straightforward at first glance, de novo transcriptome assembly and annotation can quickly prove to be challenging undertakings. In addition to familiarizing themselves with the conceptual and technical intricacies of the tasks at hand and the numerous pre- and post-processing steps involved, those interested must also grapple with an overwhelmingly large choice of tools. The lack of standardized workflows, fast pace of development of new tools and techniques and paucity of authoritative literature have served to exacerbate the difficulty of the task even further. Here, we present a comprehensive overview of de novo transcriptome assembly and annotation. We discuss the procedures involved, including pre- and post-processing steps, and present a compendium of corresponding tools.
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Venket Raghavan Louis Kraft are joint first coauthors.
Fantin Mesny and Linda Rigerte are joint second coauthors.
ISSN:1467-5463
1477-4054
1477-4054
DOI:10.1093/bib/bbab563