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cloudrnaSPAdes: Isoform assembly using bulk barcoded RNA sequencing data
Dmitry Meleshko1,2, Andrey D Prjbelski3, Mikhail Raiko4
1Tri-Institutional Computational Biology & Medicine Program, Weill Cornell Medicine of Cornell University, NY, 10021, USA.
Biorxiv : the Preprint Server for Biology
|August 7, 2023
Summary
We developed cloudrnaSPAdes, a novel RNA sequencing assembler. This tool accurately reconstructs full-length RNA isoforms from barcoded linked-read data, addressing limitations of previous methods for isoform discovery.
Area of Science:
- Genomics
- Bioinformatics
- Molecular Biology
Background:
- Long-read RNA sequencing offers full-length isoform analysis, but can be low coverage.
- Barcoded short-read RNA sequencing (e.g., 10x Genomics linked-reads) provides an alternative for high-coverage isoform studies.
- Existing pipelines struggle with barcoded short-read data and coverage gaps.
Conclusions:
- cloudrnaSPAdes provides a valuable solution for assembling isoforms from barcoded RNA-seq data.
- This advancement facilitates high-coverage, reference-free isoform discovery.
- The tool enhances the utility of barcoded RNA-seq for comprehensive transcriptomic analysis.
