A simple guide to de novo transcriptome assembly and annotation

• Published in: Briefings in bioinformatics Vol. 23; no. 2
• Main Authors: Raghavan, Venket, Kraft, Louis, Mesny, Fantin, Rigerte, Linda
• Format: Journal Article
• Language: English
• 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

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...