# Full-length isoform constructor (FLIC) – a tool for isoform discovery based on long reads

## TL;DR

FLIC is a new tool that accurately identifies full-length RNA isoforms using long-read sequencing data, especially useful for organisms with incomplete genetic information.

## Contribution

FLIC introduces a novel pipeline for isoform discovery that improves accuracy and reduces reliance on existing annotations.

## Key findings

- FLIC outperforms existing tools in reconstructing known and novel isoforms, especially without reference annotations.
- FLIC matches the accuracy of CAGE for transcription start site identification but is significantly faster.
- Evaluation on real and simulated Arabidopsis data shows FLIC's robustness and reliability.

## Abstract

Advances in high-throughput sequencing have illuminated the complexity of transcriptome landscape in eukaryotes. An inherent part of this complexity is the presence of multiple isoforms generated by the alternative splicing and the use of alternative transcription start and polyadenylation sites. However, currently available tools have limited capacity to infer full-length isoforms.

We developed a new pipeline, FLIC (full-length isoform constructor). FLIC is based on the long-read transcriptome data and integrates several key features: (1) utilizing biological replicate concordance to filter out noise and artifacts; (2) employing peak calling to precisely identify transcription start and polyadenylation sites; (3) enabling robust isoform reconstruction with minimal reliance on existing annotations. We evaluated FLIC using a dedicated set of real and simulated data of Arabidopsis thaliana cDNA sequencing. Results demonstrate that FLIC accurately reconstructs known and novel isoforms, outperforming existing tools, especially in the absence of reference annotations. A direct comparison with CAGE, currently regarded as the gold standard for transcription start site identification, shows that FLIC is equally accurate, while being much less time-consuming. Thus, FLIC provides a valuable tool for comprehensive transcript characterization, particularly for non-model organisms or when dealing with incomplete or inaccurate annotations.

FLIC is available at https://github.com/albidgy/FLIC.