MOTIVATION: Gene fusions are an important class of transcriptional variants that can influence cancer development and can be predicted from RNA sequencing (RNA-seq) data by multiple existing tools. However, the real-world performance of these tools is unclear due to the lack of known positive and negative events, especially with regard to fusion genes in individual samples. Often simulated reads are used, but these cannot account for all technical biases in RNA-seq data generated from real samples. RESULTS: Here, we present ArtiFuse, a novel approach that simulates fusion genes by sequence modification to the genomic reference, and therefore, can be applied to any RNA-seq dataset without the need for any simulated reads. We demonstrate our approach on eight RNA-seq datasets for three fusion gene prediction tools: average recall values peak for all three tools between 0.4 and 0.56 for high-quality and high-coverage datasets. As ArtiFuse affords total control over involved genes and breakpoint position, we also assessed performance with regard to gene-related properties, showing a drop-in recall value for low-expressed genes in high-coverage samples and genes with co-expressed paralogues. Overall tool performance assessed from ArtiFusions is lower compared to previously reported estimates on simulated reads. Due to the use of real RNA-seq datasets, we believe that ArtiFuse provides a more realistic benchmark that can be used to develop more accurate fusion gene prediction tools for application in clinical settings. AVAILABILITY AND IMPLEMENTATION: ArtiFuse is implemented in Python. The source code and documentation are available at https://github.com/TRON-Bioinformatics/ArtiFusion. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

SUMMARY: We have developed a laboratory information management system (LIMS) for a next-generation sequencing (NGS) laboratory within the existing Galaxy platform. The system provides lab technicians standard and customizable sample information forms, barcoded submission forms, tracking of input sample quality, multiplex-capable automatic flow cell design and automatically generated sample sheets to aid physical flow cell preparation. In addition, the platform provides the researcher with a user-friendly interface to create a request, submit accompanying samples, upload sample quality measurements and access to the sequencing results. As the LIMS is within the Galaxy platform, the researcher has access to all Galaxy analysis tools and workflows. The system reports requests and associated information to a message queuing system, such that information can be posted and stored in external systems, such as a wiki. Through an API, raw sequencing results can be automatically pre-processed and uploaded to the appropriate request folder. Developed for the Illumina HiSeq 2000 instrument, many features are directly applicable to other instruments. AVAILABILITY AND IMPLEMENTATION: The code and documentation are available at http://tron-mainz.de/tron-facilities/computational-medicine/galaxy-lims/