5.6 years ago by
Washington University School of Medicine, St. Louis, USA
FusionCatcher is another option.
FusionCatcher searches for novel/known fusion genes, translocations, and chimeras in RNA-seq data (paired-end reads from Illumina NGS platforms like Solexa and HiSeq) from diseased samples. The aims of FusionCatcher are: very good detection rate for finding candidate fusion genes, very easy to use (i.e. no a priori knowledge of databases and bioinformatics is needed in order to run FusionCatcher), to be as automatic as possible (i.e. the FusionCatcher will choose automatically the best parameters in order to find candidate fusion genes, e.g. finding automatically the adapters, building the exon-exon junctions automatically based on the length of the input reads, etc.) while providing the best possible detection rate for finding fusion genes
Current citation for FusionCatcher:
D. Nicorici, M. Satalan, H. Edgren, S. Kangaspeska, A. Murumagi, O. Kallioniemi, S. Virtanen, O. Kilkku, FusionCatcher – a tool for finding somatic fusion genes in paired-end RNA-sequencing data, bioRxiv, Nov. 2014, DOI:10.1101/011650