Reference-free discovery with barcoded single-cell sequencing

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Abstract
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).
Funding Information
  • National Institute of General Medical Sciences (R35GM139517)
  • Chan Zuckerberg Data Insights Big Ideas for Oceans grant from the Stanford Oceans Department and Stanford Woods Institute for the Environment
  • Narodowe Centrum Nauki (DEC-2022/45/B/ST6/03032)
  • Narodowe Centrum Nauki (DEC-2022/45/B/ST6/03032)
  • National Institute on Aging (R01AG076908)
  • Big Ideas for Oceans grant from the Stanford Oceans Department and Stanford Woods Institute for the Environment

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