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<p>Single-cell RNA sequencing (scRNA-seq) analyses typically focus on alignment and differential gene expression, being blind to other transcriptome variation. Here we present sc-SPLASH for statistics-first, reference-free discovery on barcoded scRNA-seq and spatial transcriptomics; its independent BKC submodule optimizes barcoded data preprocessing and is approximately 50-fold faster than UMI-tools. sc-SPLASH discovers secreted repeat proteins in immune-like cells of sponge (<i>Spongilla</i>; missing from the reference) and tunicate (<i>Ciona</i>).</p>

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Reference-free discovery with barcoded single-cell sequencing

  • 期刊论文

  • 发表日期：

    2026年4月22日

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  • Roozbeh Dehghannasiri,
  • Marek Kokot,
  • Alexander L. Starr,
  • Jamie Maziarz,
  • Tal Gordon,
  • Serena Y. Tan,
  • Peter L. Wang,
  • Ayelet Voskoboynik,
  • Jacob M. Musser,
  • Sebastian Deorowicz,
  • Julia Salzman

摘要

Single-cell RNA sequencing (scRNA-seq) analyses typically focus on alignment and differential gene expression, being blind to other transcriptome variation. Here we present sc-SPLASH for statistics-first, reference-free discovery on barcoded scRNA-seq and spatial transcriptomics; its independent BKC submodule optimizes barcoded data preprocessing and is approximately 50-fold faster than UMI-tools. sc-SPLASH discovers secreted repeat proteins in immune-like cells of sponge (Spongilla; missing from the reference) and tunicate (Ciona).