RNAfragmenter

RNAfragmenter is a software tool designed to simulate or perform fragmentation of RNA sequences in support of RNA sequencing experiment design and data analysis. By producing controlled RNA fragments, it enables researchers to evaluate how fragmentation affects downstream steps such as alignment, quantification, and transcript assembly.

The program operates as a command-line utility that accepts input RNA sequences or transcript collections in standard formats (for example FASTA or FASTQ-annotated transcripts) and generates RNA fragment sequences according to user-specified fragmentation models. Users can set a mean fragment length and a standard deviation, choose a random or end-biased cleavage model, and apply biases related to sequence context or GC content. Optional features may include simulating sequencing adapters, strand information, and quality scores. Outputs typically include fragment FASTA or FASTQ files and a summary of the simulated fragment length distribution and optional coverage estimates.

Applications include benchmarking read mappers and transcript quantification tools, testing isoform discrimination, and educating researchers about how fragmentation influences observed coverage. The tool is useful in method development pipelines, allowing one to compare the robustness of analysis methods under different fragmentation scenarios.

Limitations include the fact that in vivo and in vitro fragmentation are affected by many experimental variables that are difficult to model perfectly; RNAfragmenter provides a simplified abstraction. Users should interpret results in the context of parameter choices and complement simulations with empirical data when possible. It is typically distributed as open-source software with documentation and example datasets.