Transcriptome Assembly at Single-Cell Resolution with Beaver.

ABSTRACT: Emerging single-cell RNA sequencing techniques (scRNA-seq) has enabled the study of cellular transcriptome heterogeneity, yet accurate reconstruction of full-length transcripts at single-cell resolution remains challenging due to high dropout rates and sparse coverage. While meta-assembly approaches offer promising solutions by integrating information across multiple cells, current methods struggle to balance consensus assembly with cell-specific transcriptional signatures. Here, we present Beaver, a cell-specific transcript assembler designed for short-read scRNA-seq data. Beaver implements a transcript fragment graph to organize individual assemblies and designs an efficient dynamic programming algorithm that searches for candidate full-length transcripts from the graph. Beaver incorpora

SUBMITTER: Shi Q 

PROVIDER: S-EPMC11580954 | biostudies-literature | 2024 Nov

REPOSITORIES: biostudies-literature