SUMMARY: Presence or absence of gene fusions is one of the most important diagnostic markers in many cancer types. Consequently, fusion detection methods using various genomics data types, such as RNA sequencing (RNA-seq) are valuable tools for research and clinical applications. While information-rich RNA-seq data have proven to be instrumental in discovery of a number of hallmark fusion events, bioinformatics tools to detect fusions still have room for improvement. Here, we present Fusion-Bloom, a fusion detection method that leverages recent developments in de novo transcriptome assembly and assembly-based structural variant calling technologies (RNA-Bloom and PAVFinder, respectively). We benchmarked Fusion-Bloom against the performance of five other state-of-the-art fusion detection tools using multiple datasets. Overall, we observed Fusion-Bloom to display a good balance between detection sensitivity and specificity. We expect the tool to find applications in translational research and clinical genomics pipelines. AVAILABILITY AND IMPLEMENTATION: Fusion-Bloom is implemented as a UNIX Make utility, available at https://github.com/bcgsc/pavfinder and released under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

MOTIVATION: A considerable amount of human intervention is currently required to produce high-quality fingerprint-based physical maps for genomic studies. RESULTS: An algorithm has been developed and implemented to automatically order fingerprinted clones within contigs. The resulting software, named CORAL (Clone ORdering ALgorithm), has been tested on maps that have previously been manually edited and on maps derived from in silico simulations. The fingerprint map and DNA sequence of the human genome has provided an additional test to CORAL. Measurements suggest that CORAL performs significantly better than the software currently used by most laboratories to order fingerprinted clones at throughputs far exceeding those that can be achieved manually.