FusionCatcher searches for novel/known somatic fusion genes, translocations, and
chimeras in RNA-seq data (paired-end or single-end reads from Illumina NGS platforms
like Solexa/HiSeq/NextSeq/MiSeq/MiniSeq) from diseased/cancer samples.
The aims of FusionCatcher are:
very good detection rate for finding candidate somatic fusion
genes (see somatic mutations; using a matched normal sample is
optional; several databases of known fusion genes found in healthy
samples are used as a list of known false positives; biological
knowledge is used, like for example gene fusion between a gene and
its pseudogene is filtered out),
very good RT-PCR validation rate of found candidate somatic fusion
genes (this is very important for us),
very easy to use (i.e. no a priori knowledge of bioinformatic
databases and bioinformatics is needed in order to run FusionCatcher BUT
Linux/Unix knowledge is needed; it allows a very high level of control
for expert users),
to be as automatic as possible (i.e. choose automatically the best
parameters for the given input data, e.g. finding automatically the
adapters, quality trimming of reads, building the exon-exon junctions
automatically based on the length of the reads given as input, etc.
whilst giving full control to expert users) whilst providing the best
possible detection rate for finding somatic fusion genes (with very
low rate of false positives and very good sensitivity).
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