biostudies-literatureUnknown14(5)Wang YRNA sequencing (RNA-seq) is a high-throughput technology that provides in-depth information on transcriptome. The advancement and dropping costs of RNA sequencing, accompanied by more available reference genomes for different species, make transcriptome analysis in non-model organisms possible. Current obstacles in analyzing RNA-seq data include a lack of functional annotation, which may complicate the process of linking genes to corresponding functions. Here, we provide a one-stop RNA-seq analysis pipeline, PipeOne-NM, for transcriptome functional annotation, non-coding RNA identification, and transcripts alternative splicing analysis of non-model organisms, intended for use with Illumina platform-based RNA-seq data. We performed PipeOne-NM on 237 <i>Schmidtea mediterranea</i> RNA-seq runGenes989https://www.ebi.ac.uk/biostudies/studies/S-EPMC10218480biostudies-literatureComprehensive RNA-Seq Analysis Pipeline for Non-Model Organisms and Its Application in <i>Schmidtea mediterranea</i>.PMC10218480Xiong YSongyang ZLi SNong BXu SZhou WWang YfalseComprehensive RNA-Seq Analysis Pipeline for Non-Model Organisms and Its Application in <i>Schmidtea mediterranea</i>.RNA sequencing (RNA-seq) is a high-throughput technology that provides in-depth information on transcriptome. The advancement and dropping costs of RNA sequencing, accompanied by more available reference genomes for different species, make transcriptome analysis in non-model organisms possible. Current obstacles in analyzing RNA-seq data include a lack of functional annotation, which may complicate the process of linking genes to corresponding functions. Here, we provide a one-stop RNA-seq analysis pipeline, PipeOne-NM, for transcriptome functional annotation, non-coding RNA identification, and transcripts alternative splicing analysis of non-model organisms, intended for use with Illumina platform-based RNA-seq data. We performed PipeOne-NM on 237 <i>Schmidtea mediterranea</i> RNA-seq run2023-01-01T00:00:00Z2023 Apr2025-04-05T14:15:34.353Z2025-04-05T14:15:34.353ZS-EPMC102184803723935010.3390/genes14050989