tRNAnalysis: A flexible pre-processing and next-generation sequencing data analysis pipeline for transfer RNA

Abstract

Many tools have been developed to analyse small RNA sequencing data, however it remains a challenging task to accurately process reads aligning to small RNA due to their short-read length. Most pipelines have been developed with miRNA analysis in mind and there are currently very few workflows focused on the analysis of transfer RNAs. Moreover, these workflows suffer from being low throughput, difficult to install and lack sufficient visualisation to make the output interpretable. To address these issues, we have built a comprehensive and customisable small RNA-seq data analysis pipeline, with emphasis on the analysis of tRNAs. The pipeline takes as an input a fastq file of small RNA sequencing reads and performs successive steps of mapping and alignment to transposable elements, gene transcripts, miRNAs, snRNAs, rRNA and tRNAs. Subsequent steps are then performed to generate summary statistics on reads of tRNA origin, which are then visualised in a html report. Unlike other low-throughput analysis tools currently available, our high-throughput method allows for the simultaneous analysis of multiple samples and scales with the number of input files. tRNAnalysis is command line runnable and is implemented predominantly using Python and R. The source code is available at https://github.com/Acribbs/tRNAnalysis.