transXpress: a Snakemake pipeline for streamlined de novo transcriptome assembly and annotation
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12859_2023_Article_5254.pdf
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Author(s)
Fallon, Timothy R.
Čalounová, Tereza
Mokrejš, Martin
Weng, Jing-Ke
Pluskal, Tomáš
Date Issued
April 4, 2023
Publisher
BioMed Central
Citation
BMC Bioinformatics. 2023 Apr 04;24(1):133
Version
Final published version
Abstract
Abstract
Background
RNA-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.
Results
Here 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.
Conclusions
transXpress 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.
MIT Department
Massachusetts Institute of Technology. Department of Biology
Whitehead Institute for Biomedical Research
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Creative Commons Attribution
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DOI of Published Version
https://doi.org/10.1186/s12859-023-05254-8
