rRNA

rsRNAfinder Toolkit

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If you are using this toolkit, please cite: Comprehensive profiling of rRNA-derived small RNAs in Arabidopsis thaliana using rsRNAfinder pipeline
Kalakoti, G., Vivek, A. T., Kamboj, A., Singh, A., Chakraborty, S., Kumar, S. (2024) MethodsX, 12, 102494

Welcome to rsRNAfinder Toolkit

rsRNAfinder Toolkit identifies and annotates ribosomal RNA-derived small RNAs (rsRNAs), categorizing them into three series: rRF-5, rRF-3, and rRF-i. This analytical approach enables robust identification of rsRNAs using sRNA-seq datasets from Arabidopsis thaliana. It provides
comprehensive information of identified rsRNAs including rsRNA category, expression, size, and parent rRNA details. The pipeline is implemented using Python and Bash, rsRNAfinder utilizes the snakemake workflow management system.


You can clone the repository from GitHub Logo

workflow


sRNA-seq data analysis

Performs in-depth analysis of reference-aligned sRNA-seq data, facilitating rsRNA annotation and quantification


Parametric reporting

Reports with parameters such as rsRNA size distributions, strandedness, genomic origin, and source rRNA origin


Illustrative validation

Validation uncovers distinct rsRNAs from all rRNA types, distinguished by unique identity, abundance, and length