ArticleNature biotechnology2025
Scalable and unsupervised discovery from raw sequencing reads using SPLASH2.
Article in Nature biotechnology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- MKMC enables reference-free transcriptomic analysis using k-mer representations.bioRxiv : the preprint server for biology · 2026Article
- Reference-free discovery with barcoded single-cell sequencing.Nature biotechnology · 2026Article
- Comparison of hybrid-and mono-pathotype Escherichia coli isolates from South Korea based on whole genome analysis and cytotoxicity assay.Journal of biomedical science · 2026Article
- A Reference-Free Algorithm Discovers Regulation in the Plant Transcriptome.Plant direct · 2026Article
- Pretraining and the lasso.Journal of the Royal Statistical Society. Series B, Statistical methodology · 2026Article
- Viroid-like colonists of human microbiomes.Cell · 2024Article
- Article
- OASIS: An interpretable, finite-sample valid alternative to Pearson'sbioRxiv : the preprint server for biology · 2023Article
- SPLASH: a statistical, reference-free genomic algorithm unifies biological discovery.bioRxiv : the preprint server for biology · 2023Article
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Authors and funding
5 authors.
Funding
Abstract
We introduce SPLASH2, a fast, scalable implementation of SPLASH based on an efficient k-mer counting approach for regulated sequence variation detection in massive datasets from a wide range of sequencing technologies and biological contexts. We demonstrate biological discovery by SPLASH2 in single-cell RNA sequencing (RNA-seq) data and in bulk RNA-seq data from the Cancer Cell Line Encyclopedia, including unannotated alternative splicing in cancer transcriptomes and sensitive detection of circular RNA.
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