ArticleBMC bioinformatics2023
transXpress: a Snakemake pipeline for streamlined de novo transcriptome assembly and annotation.
Article in BMC bioinformatics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Guidelines to Study Transcriptome Remodeling by Proteins Using Deep Sequencing (RNA-Seq).Methods in molecular biology (Clifton, N.J.) · 2027Article
- Spatial proteomics in precision medicine: technologies, bioinformatics, and translational applications.Precision clinical medicine · 2026Review
- CRESCENT, a comprehensive RNA-Seq expression, splicing, and coding/non-coding element network tool.BMC bioinformatics · 2026Article
- Pipeasm: a tool for automated large chromosome-scale genome assembly and evaluation.Bioinformatics advances · 2026Article
- Proteogenomic approach to immunopeptidomics of ovarian tumors identifies shared peptide vaccine candidates.NPJ vaccines · 2025Article
- HPC-T-Assembly: a pipeline for de novo transcriptome assembly of large multi-specie datasets.BMC bioinformatics · 2025Article
- The emergence and loss of cyclic peptides inProceedings of the National Academy of Sciences of the United States of America · 2025Article
- Semblans: automated assembly and processing of RNA-seq data.Bioinformatics (Oxford, England) · 2024Article
- TrAnnoScope: A Modular Snakemake Pipeline for Full-Length Transcriptome Analysis and Functional Annotation.Genes · 2024Article
- HPC-T-Annotator: an HPC tool for de novo transcriptome assembly annotation.BMC bioinformatics · 2024Article
- Comprehensive Analysis of the Influence of Technical and Biological Variations on De Novo Assembly of RNA-Seq Datasets.Bioinformatics and biology insights · 2024Article
- Emerging functions within the enzyme families of plant alkaloid biosynthesis.Phytochemistry reviews : proceedings of the Phytochemical Society of Europe · 2023Article
- TAGADA: a scalable pipeline to improve genome annotations with RNA-seq data.NAR genomics and bioinformatics · 2023Article
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5 authors.
Funding
Abstract
backgroundRNA-seq followed by de novo transcriptome assembly has been a transformative technique in biological research of non-model organisms, but the computational processing of RNA-seq data entails many different software tools. The complexity of these de novo transcriptomics workflows therefore presents a major barrier for researchers to adopt best-practice methods and up-to-date versions of software.
resultsHere we present a streamlined and universal de novo transcriptome assembly and annotation pipeline, transXpress, implemented in Snakemake. transXpress supports two popular assembly programs, Trinity and rnaSPAdes, and allows parallel execution on heterogeneous cluster computing hardware.
conclusionstransXpress simplifies the use of best-practice methods and up-to-date software for de novo transcriptome assembly, and produces standardized output files that can be mined using SequenceServer to facilitate rapid discovery of new genes and proteins in non-model organisms.
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