SeekFusion - A clinically validated fusion transcript detection pipeline for PCR-based next-generation sequencing of RNA.

In this project, we describe SeekFusion, a time-efficient pipeline that leverages de novo assembly and alignment based approaches toaccurately identify gene fusions utilizing PCR-UMI-based amplicon RNA-Seq.Seekfusion is a time-efficient pipeline that leverages de novo assembly and alignment based approaches to accurately identify gene fusions utilizing PCR-UMI-based amplicon RNA-Seq. SeekFusion performs rapid alignment to gene sequences, then groups and filters aligned reads for de novo assembly. Assembled contigs are realigned to a reference genome and fusion genes are identified, annotated and reported in a widely accepted VCF format. Using verified cases and synthetic controls, we demonstrate that SeekFusion outperforms existing pipelines by balancing high analytical sensitivity and specificity with computational efficiency.The files deposited here are fastq raw sequence data used for benchmarking the pipeline against popular methods such as STAR Fusion, Tophat fusion and JAFFA.The dataset provided in this study is from a targeted RNA assay using Qiaseq RNA chemistry. This dataset provides means to benchmark fusion detection pipelines designed to work on PCR based targeted RNA assays.