nihilee/fusioncatcher

Finder of Somatic Fusion Genes in RNA-seq data

FusionCatcher

Finder of somatic fusion-genes in RNA-seq data.

Download / Install / Update / Upgrade FusionCatcher

Use this one-line command:

wget http://sf.net/projects/fusioncatcher/files/bootstrap.py -O bootstrap.py && python bootstrap.py -t --download

If one wants to have all the questions asked by boostrap.py answered automatically with yes then add -y to the command above. For more installing options, see:

bootstrap.py --help

On Ubuntu Linux running this command before installing FusionCatcher using bootstrap.py would help making the installation process smoother:

sudo apt-get install wget gawk gcc g++ make cmake automake curl unzip zip bzip2 tar gzip pigz parallel build-essential libncurses5-dev libc6-dev zlib1g zlib1g-dev libtbb-dev libtbb2 python python-dev python-numpy python-biopython python-xlrd python-openpyxl default-jdk

FusionCatcher can be installed also using conda, as follows:

conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
conda create -n fusioncatcher fusioncatcher
source activate fusioncatcher
download-human-db.sh

FusionCatcher can be installed also from GitHub, as follows:

git clone https://github.com/ndaniel/fusioncatcher
cd fusioncatcher/tools/
./install_tools.sh
cd ../data
./download-human-db.sh

NOTE: Here it is assumed that Python 2.7.x, BioPython (>v1.5), and Java Runtime Environment 1.8 are already installed.

Description

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 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 good detection of challenging fusion genes, like for example IGH fusions, CIC fusions, DUX4 fusions, CRLF2 fusions, TCF3 fusions, etc.
• 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. the FusionCatcher will choose automatically the best parameters in order to find candidate somatic fusion genes, 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. while giving also full control to expert users) while providing the best possible detection rate for finding somatic fusion genes (with a very low rate of false positives but a very good precision).

Manual

A detailed manual is available here.

Forum

A forum for FusionCatcher is available at Google Groups.

Release history

A complete release history can be found here.

Official releases

Old releases and the latest official release of FusionCatcher are on https://sourceforge.net/projects/fusioncatcher/files/

Citing

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