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transXpress: a Snakemake pipeline for streamlined de novo transcriptome assembly and annotation
Timothy R Fallon1, Tereza Čalounová2, Martin Mokrejš2
1Scripps Institution of Oceanography, UC San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, USA.
BMC Bioinformatics
|April 4, 2023
Summary
A new pipeline, transXpress, simplifies de novo transcriptome assembly for non-model organisms. It integrates best-practice tools, enabling faster gene discovery by streamlining RNA-seq data analysis.
Area of Science:
- Bioinformatics
- Genomics
- Computational Biology
Background:
- RNA sequencing (RNA-seq) and de novo transcriptome assembly are crucial for studying non-model organisms.
- Complex computational workflows and numerous software tools hinder the adoption of best practices in transcriptomics.
Purpose of the Study:
- To develop a streamlined and universal pipeline for de novo transcriptome assembly and annotation.
- To simplify the use of best-practice and up-to-date software for researchers working with non-model organisms.
Main Methods:
- The transXpress pipeline is implemented in Snakemake.
- It supports popular assembly programs like Trinity and rnaSPAdes.
- The pipeline allows for parallel execution on heterogeneous cluster computing hardware.
Main Results:
- transXpress offers a simplified approach to de novo transcriptome assembly.
- It supports multiple assembly programs and parallel processing.
- The pipeline produces standardized output files.
Conclusions:
- transXpress facilitates the use of advanced methods and current software for de novo transcriptome assembly.
- Standardized output aids in rapid gene and protein discovery in non-model organisms using tools like SequenceServer.
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