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transXpress: a Snakemake pipeline for streamlined de novo transcriptome assembly and annotation
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 therefor...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10074830/ https://www.ncbi.nlm.nih.gov/pubmed/37016291 http://dx.doi.org/10.1186/s12859-023-05254-8 |
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author | Fallon, Timothy R. Čalounová, Tereza Mokrejš, Martin Weng, Jing-Ke Pluskal, Tomáš |
author_facet | Fallon, Timothy R. Čalounová, Tereza Mokrejš, Martin Weng, Jing-Ke Pluskal, Tomáš |
author_sort | Fallon, Timothy R. |
collection | PubMed |
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. |
format | Online Article Text |
id | pubmed-10074830 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-100748302023-04-06 transXpress: a Snakemake pipeline for streamlined de novo transcriptome assembly and annotation Fallon, Timothy R. Čalounová, Tereza Mokrejš, Martin Weng, Jing-Ke Pluskal, Tomáš BMC Bioinformatics Software 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. BioMed Central 2023-04-04 /pmc/articles/PMC10074830/ /pubmed/37016291 http://dx.doi.org/10.1186/s12859-023-05254-8 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data. |
spellingShingle | Software Fallon, Timothy R. Čalounová, Tereza Mokrejš, Martin Weng, Jing-Ke Pluskal, Tomáš transXpress: a Snakemake pipeline for streamlined de novo transcriptome assembly and annotation |
title | transXpress: a Snakemake pipeline for streamlined de novo transcriptome assembly and annotation |
title_full | transXpress: a Snakemake pipeline for streamlined de novo transcriptome assembly and annotation |
title_fullStr | transXpress: a Snakemake pipeline for streamlined de novo transcriptome assembly and annotation |
title_full_unstemmed | transXpress: a Snakemake pipeline for streamlined de novo transcriptome assembly and annotation |
title_short | transXpress: a Snakemake pipeline for streamlined de novo transcriptome assembly and annotation |
title_sort | transxpress: a snakemake pipeline for streamlined de novo transcriptome assembly and annotation |
topic | Software |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10074830/ https://www.ncbi.nlm.nih.gov/pubmed/37016291 http://dx.doi.org/10.1186/s12859-023-05254-8 |
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