TAGADA: a scalable pipeline to improve genome annotations with RNA-seq data.

ABSTRACT: Genome annotation plays a crucial role in providing comprehensive catalog of genes and transcripts for a particular species. As research projects generate new transcriptome data worldwide, integrating this information into existing annotations becomes essential. However, most bioinformatics pipelines are limited in their ability to effectively and consistently update annotations using new RNA-seq data. Here we introduce TAGADA, an RNA-seq pipeline for Transcripts And Genes Assembly, Deconvolution, and Analysis. Given a genomic sequence, a reference annotation and RNA-seq reads, TAGADA enhances existing gene models by generating an improved annotation. It also computes expression values for both the reference and novel annotation, identifies long non-coding transcripts (lncRNAs), and provid

SUBMITTER: Kurylo C 

PROVIDER: S-EPMC10578202 | biostudies-literature | 2023 Dec

REPOSITORIES: biostudies-literature