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bioRxiv · 10.1101/2025.05.28.656613

HAMRLNC: A Comprehensive Pipeline for High-throughput Analysis of Modified Ribonucleotides and Long Non-Coding Ribonucleic Acids

Obih, C. E.·Li, J.·melandri, G.·Pauli, D.·Lyons, E.·Nelson, A. D. L.·Gregory, B. D.
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Abstract

As sequencing technologies advance and costs decline, there has been a surge in the application of RNA sequencing (RNA-seq) in understanding biological processes. In addition to the typical uses of RNA-seq for transcriptomics, gene annotation, novel gene discovery, and network analysis, these data can enable a deeper understanding of cellular processes through the identification of RNA modifications (epitranscriptome) and long non-coding RNAs (lncRNAs). To expedite discovery, we developed a portable, centralized computational pipeline for High-throughput Annotation of Modified Ribonucleotides and Long Non-Coding ribonucleic acids (HAMRLNC). HAMRLNC differs from existing methods by incorporating three workflows for quantifying transcript abundance, inferring RNA modifications, and lncRNA annotation using the same RNA- seq pre-processing and mapping steps. This facilitates reproducibility across multiple analyses and allows researchers to perform post-hoc analyses of archived sequencing data. In addition, we include novel analysis features to enable downstream visualization of annotated modified RNAs. HAMRLNC generates over a dozen well-defined and labeled figures as output, including gene ontology heatmaps, modification enrichment landscape, and modification clustering statistics. Availability and ImplementationHAMRLNC is an open-source software, and the source code is available at https://github.com/bdgregory/HAMRLNC. The pipeline can be installed and used through a docker container (https://hub.docker.com/r/chosenobih/HAMRLNC/tags). HAMRLNC is also available as an app in the CyVerse Discovery Environment https://de.cyverse.org/. Supplementary informationSupplementary data are available at BioRxiv online.

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Obih, C. E., Li, J., melandri, G., Pauli, D., Lyons, E., Nelson, A. D. L., Gregory, B. D.. 2025-06-01. HAMRLNC: A Comprehensive Pipeline for High-throughput Analysis of Modified Ribonucleotides and Long Non-Coding Ribonucleic Acids. https://doi.org/10.1101/2025.05.28.656613

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