rnaspades
Key Features:
- SPAdes-Based Assembly Engine: Extends the SPAdes assembler to transcriptomics, addressing non-uniform read coverage, sequencing errors, and chimeric reads in RNA-Seq datasets.
- Improved Assembly Accuracy: Generates accurate transcriptome assemblies with performance improvements over E+V-SC, Velvet, and SoapDeNovo, supporting reconstruction without a reference genome.
Scientific Applications:
- De Novo Transcriptome Reconstruction: Assembles transcriptomes for organisms lacking reference genomes, enabling gene expression analysis, novel transcript discovery, and metagenomic characterization of uncultivable organisms.
Methodology:
rnaspades applies SPAdes graph-based assembly algorithms to RNA-Seq reads, incorporating error correction and coverage-aware strategies to reconstruct transcripts de novo under variable expression levels and sequencing artifacts.
Topics
Collections
Details
- Maturity:
- Mature
- Tool Type:
- web application
- Operating Systems:
- Linux, Windows, Mac
- Added:
- 12/19/2016
- Last Updated:
- 11/24/2024
Operations
Data Inputs & Outputs
De-novo assembly
Publications
Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA. SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing. Journal of Computational Biology. 2012;19(5):455-477. doi:10.1089/cmb.2012.0021. PMID:22506599. PMCID:PMC3342519.
Afgan E, Baker D, van den Beek M, Blankenberg D, Bouvier D, Čech M, Chilton J, Clements D, Coraor N, Eberhard C, Grüning B, Guerler A, Hillman-Jackson J, Von Kuster G, Rasche E, Soranzo N, Turaga N, Taylor J, Nekrutenko A, Goecks J. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update. Nucleic Acids Research. 2016;44(W1):W3-W10. doi:10.1093/nar/gkw343. PMID:27137889. PMCID:PMC4987906.
Mareuil F, Doppelt-Azeroual O, Ménager H. A public Galaxy platform at Pasteur used as an execution engine for web services. Unknown Journal. 2017. doi:10.7490/f1000research.1114334.1.