transXpress: a Snakemake pipeline for streamlined de novo transcriptome assembly and annotation

Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61388963%3A_____%2F23%3A00571021" target="_blank" >RIV/61388963:_____/23:00571021 - isvavai.cz</a>
Result on the web
<a href="https://doi.org/10.1186/s12859-023-05254-8" target="_blank" >https://doi.org/10.1186/s12859-023-05254-8</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1186/s12859-023-05254-8" target="_blank" >10.1186/s12859-023-05254-8</a>

Result language
angličtina
Original language name
transXpress: a Snakemake pipeline for streamlined de novo transcriptome assembly and annotation
Original language description
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.
Czech name
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Czech description
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Type
J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database
CEP classification
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OECD FORD branch
10201 - Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8)

Project
<a href="/en/project/GM21-11563M" target="_blank" >GM21-11563M: Mapping the chemodiversity of Piperaceae plants using next-generation MZmine platform</a><br>
Continuities
I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Publication year
2023
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

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