Systematic assessment of long-read RNA-seq methods for transcript identification and quantification

Nature Methods, Год журнала: 2024, Номер 21(7), С. 1349 - 1363

Опубликована: Июнь 7, 2024

Abstract The Long-read RNA-Seq Genome Annotation Assessment Project Consortium was formed to evaluate the effectiveness of long-read approaches for transcriptome analysis. Using different protocols and sequencing platforms, consortium generated over 427 million sequences from complementary DNA direct RNA datasets, encompassing human, mouse manatee species. Developers utilized these data address challenges in transcript isoform detection, quantification de novo detection. study revealed that libraries with longer, more accurate produce transcripts than those increased read depth, whereas greater depth improved accuracy. In well-annotated genomes, tools based on reference demonstrated best performance. Incorporating additional orthogonal replicate samples is advised when aiming detect rare novel or using reference-free approaches. This collaborative offers a benchmark current practices provides direction future method development

Язык: Английский

Systematic assessment of long-read RNA-seq methods for transcript identification and quantification

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown

Опубликована: Июль 27, 2023

Abstract The Long-read RNA-Seq Genome Annotation Assessment Project (LRGASP) Consortium was formed to evaluate the effectiveness of long-read approaches for transcriptome analysis. consortium generated over 427 million sequences from cDNA and direct RNA datasets, encompassing human, mouse, manatee species, using different protocols sequencing platforms. These data were utilized by developers address challenges in transcript isoform detection quantification, as well de novo identification. study revealed that libraries with longer, more accurate produce transcripts than those increased read depth, whereas greater depth improved quantification accuracy. In well-annotated genomes, tools based on reference demonstrated best performance. When aiming detect rare novel or when reference-free approaches, incorporating additional orthogonal replicate samples are advised. This collaborative offers a benchmark current practices provides direction future method development

Язык: Английский

Transcriptomics in the era of long-read sequencing

Nature Reviews Genetics, Год журнала: 2025, Номер unknown

Опубликована: Март 28, 2025

Язык: Английский