A comprehensive pipeline for genome annotation across species: a case study onSchmidtea mediterranea
Abstract
Background
Despite advancements in genome annotation tools, challenges persist for non-classical model organisms with limited genomic resources, such asSchmidtea mediterranea.
Findings
To address these challenges, we developed a flexible and scalable genome annotation pipeline that integrates short-read (Illumina) and long-read (PacBio) sequencing technologies. The pipeline combines reference-based andde novoassembly methods, effectively handling genomic variability and alternative splicing events. Functional annotation is conducted to filter out low-confidence transcripts and ensure biological relevance. Applying this pipeline to the asexual strain ofS. mediterranearevealed thousands of previously undescribed putative genes and transcripts, and improved the existing gene models, highlighting its utility in annotating complex, underexplored genomes.
Conclusions
The modularity and comprehensiveness of our pipeline ensure its adaptability for genome annotation across diverse species, making it a valuable tool for annotating genomes of non-model organisms and supporting broader genomic research. The source code and implementation details are available at<ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="https://github.com/Norreanea/SmedAnno">https://github.com/Norreanea/SmedAnno</ext-link>.
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