| Title: |
transXpress: a Snakemake pipeline for streamlined de novo transcriptome assembly and annotation |
| Authors: |
Fallon, Timothy R; Fallon, Timothy R; Čalounová, Tereza; Mokrejš, Martin; Weng, Jing-Ke; Pluskal, Tomáš |
| Source: |
BMC Bioinformatics; vol 24, iss 1, 133; 1471-2105 |
| Publisher Information: |
eScholarship, University of California 2023-01-01 |
| Document Type: |
Electronic Resource |
| Abstract: |
BackgroundRNA-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.ResultsHere 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.ConclusionstransXpress 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. |
| Index Terms: |
Biological Sciences; Bioinformatics and Computational Biology; Genetics; Bioengineering; Human Genome; Generic health relevance; Transcriptome; Sequence Analysis; RNA; RNA-Seq; Software; Gene Expression Profiling; Molecular Sequence Annotation; De novo transcriptome assembly; RNA-seq; Non-model organisms; Transcriptome annotation; Differential expression analysis; Reproducible software; High-performance computing; Mathematical Sciences; Information and Computing Sciences; Bioinformatics; Biological sciences; Information and computing sciences; Mathematical sciences; article |
| URL: |
https://escholarship.org/uc/item/40m1r17j; https://escholarship.org/content/qt40m1r17j/qt40m1r17j.pdf |
| Availability: |
Open access content. Open access content; CC-BY |
| Note: |
application/pdf; BMC Bioinformatics vol 24, iss 1, 133 1471-2105 |
| Other Numbers: |
CDLER oai:escholarship.org:ark:/13030/qt40m1r17j; qt40m1r17j; https://escholarship.org/uc/item/40m1r17j; https://escholarship.org/content/qt40m1r17j/qt40m1r17j.pdf; info:doi/10.1186/s12859-023-05254-8; https://escholarship.org/; 1453615907 |
| Contributing Source: |
UC MASS DIGITIZATION; From OAIster®, provided by the OCLC Cooperative. |
| Accession Number: |
edsoai.on1453615907 |
| Database: |
OAIster |