transXpress: a Snakemake pipeline for streamlined de novo transcriptome assembly and annotation
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...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2023-04-01
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| Series: | BMC Bioinformatics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12859-023-05254-8 |
| _version_ | 1797849863493255168 |
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| author | Timothy R. Fallon Tereza Čalounová Martin Mokrejš Jing-Ke Weng Tomáš Pluskal |
| author_facet | Timothy R. Fallon Tereza Čalounová Martin Mokrejš Jing-Ke Weng Tomáš Pluskal |
| author_sort | Timothy R. Fallon |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-09T18:51:04Z |
| format | Article |
| id | doaj.art-d93eded9aae04aa187bcae13e6236923 |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-04-09T18:51:04Z |
| publishDate | 2023-04-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-d93eded9aae04aa187bcae13e62369232023-04-09T11:28:28ZengBMCBMC Bioinformatics1471-21052023-04-0124111110.1186/s12859-023-05254-8transXpress: a Snakemake pipeline for streamlined de novo transcriptome assembly and annotationTimothy R. Fallon0Tereza Čalounová1Martin Mokrejš2Jing-Ke Weng3Tomáš Pluskal4Scripps Institution of Oceanography, UC San DiegoInstitute of Organic Chemistry and Biochemistry of the Czech Academy of SciencesInstitute of Organic Chemistry and Biochemistry of the Czech Academy of SciencesWhitehead Institute for Biomedical ResearchInstitute of Organic Chemistry and Biochemistry of the Czech Academy of SciencesAbstract 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.https://doi.org/10.1186/s12859-023-05254-8De novo transcriptome assemblyRNA-seqNon-model organismsTranscriptome annotationDifferential expression analysisReproducible software |
| spellingShingle | Timothy R. Fallon Tereza Čalounová Martin Mokrejš Jing-Ke Weng Tomáš Pluskal transXpress: a Snakemake pipeline for streamlined de novo transcriptome assembly and annotation BMC Bioinformatics De novo transcriptome assembly RNA-seq Non-model organisms Transcriptome annotation Differential expression analysis Reproducible software |
| 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 | De novo transcriptome assembly RNA-seq Non-model organisms Transcriptome annotation Differential expression analysis Reproducible software |
| url | https://doi.org/10.1186/s12859-023-05254-8 |
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