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Updated: May 5, 2026

Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution

Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution

Published on: February 24, 2015

RUMINA: deduplicación de UMI de alto rendimiento para secuenciación de amplicones y genoma completo con corrección de

E Piliper¹, S Goya¹, A L Greninger^1,2

¹Department of Laboratory Medicine and Pathology, University of Washington Medical Center, Seattle, 98109, USA.

Bioinformatics (Oxford, England)

|February 24, 2026

Abstracto

Motivation:

Unique molecular identifiers (UMIs) are widely used in next-generation sequencing to enable accurate molecular counting and error correction. However, challenges remain in accurately collapsing UMI clusters, especially when read counts are low or sparse read clusters arise from barcode sequencing errors.

Results:

We present RUMINA, a Rust-based pipeline for UMI-aware deduplication and error correction, optimized for both amplicon and shotgun sequencing. RUMINA supports multiple UMI cluster strategies, alongside majority-rule read selection independent of mapping quality, as well as discrete handling of 1-2 read clusters, paired-end merging, and read-length stratification. Benchmarking using simulated HIV population sequencing data and real-world iCLIP and TCR datasets showed that RUMINA improves ultra-low frequency SNV detection (0.01-1%), reduces false positives, enhances reproducibility, and processes sequencing data up to 10-fold faster than existing tools. By integrating UMI- and sequence-level correction in a high-performance framework, RUMINA offers a fast, scalable, and robust solution for UMI-enabled sequencing workflows.

Availability:

RUMINA is implemented in Rust and distributed as open-source code and precompiled binaries. Source code and installation instructions are available at https://github.com/greninger-lab/rumina. Documentation associated with this manuscript is available at https://github.com/greninger-lab/rumina_paper.

Supplementary Information:

Supplementary data are available at Bioinformatics online.

Palabras clave:

deduplicación de UMI corrección de errores secuenciación de próxima generación análisis de genoma completo bioinformática RUMINA

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