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bioRxiv · 10.1101/2023.03.17.533189

NOMAD2 provides ultra-efficient, scalable, and unsupervised discovery on raw sequencing reads

Kokot, M.·Dehghannasiri, R.·Baharav, T. Z.·Salzman, J.·Deorowicz, S.
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Abstract

SPLASH is an unsupervised, reference-free, and unifying algorithm that discovers regulated sequence variation through statistical analysis of k-mer composition, subsuming many application-specific methods. Here, we introduce SPLASH2, a fast, scalable implementation of SPLASH based on an efficient k-mer counting approach. SPLASH2 enables rapid analysis of massive datasets from a wide range of sequencing technologies and biological contexts, delivering unparalleled scale and speed. The SPLASH2 algorithm unveils new biology (without tuning) in single-cell RNA-sequencing data from human muscle cells, as well as bulk RNA-seq from the entire Cancer Cell Line Encyclopedia (CCLE), including substantial unannotated alternative splicing in cancer transcriptome. The same untuned SPLASH2 algorithm recovers the BCR-ABL gene fusion, and detects circRNA sensitively and specifically, underscoring SPLASH2s unmatched precision and scalability across diverse RNA-seq detection tasks.

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Kokot, M., Dehghannasiri, R., Baharav, T. Z., Salzman, J., Deorowicz, S.. 2023-03-21. NOMAD2 provides ultra-efficient, scalable, and unsupervised discovery on raw sequencing reads. https://doi.org/10.1101/2023.03.17.533189

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