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FusionCaller

Gene fusion detection.

The component includes 5 different tools (FusionCatcher, ChimeraScan, deFuse, SOAPfuse, EricScript) for gene fusion detection from RNA-Seq paired-end input reads. It is suggested to use the very raw reads without trimming since the tools perform their own trimming and quality filters on the reads in the early stages of their pipelines.

Before run the compenent install the fusion detection tool you want to use and create its genome database with the respective installation scripts in $ANDURIL_HOME/bundles/sequencing/lib/install_scripts/. The component requires the dependecies that the single fusion detection tool require (see the official documentation of each tool for more information).

Dependencies:

--------------> FusionCatcher (https://github.com/ndaniel/fusioncatcher) Python 2.7.6 (>=2.6.0 and < 3.0 is fine)

--------------> deFuse (https://bitbucket.org/dranew/defuse) To build the deFuse toolset you must have the boost c++ development libraries installed. A full install of boost is not required. The easiest thing to do is to download the latest boost source tar.gz, extract it, then add the extracted path to the CPLUS_INCLUDE_PATH environment variable (in bash, export CPLUS_INCLUDE_PATH=/boost/directory/:$CPLUS_INCLUDE_PATH). Additionaly it requires: R, Rscript, R ada package, bowtie, bowtie-build, bwa, blat, faToTwoBit, gmap, gmap_build installed and present in $PATH. To install the ada package run R, then at the prompt type install.packages("ada")

--------------> EricScript (https://sourceforge.net/projects/ericscript) Perl Requires R, ada package, bwa, Bedtools, Seqtk, BLAT installed and present in $PATH.

--------------> ChimeraScan (https://code.google.com/archive/p/chimerascan/) Python >=2.6 Additionaly it requires: Pysam, bowtie, bowtie-build installed and present in $PATH.

--------------> SOAPfuse (https://sourceforge.net/projects/soapfuse) Perl >=5.8.5

Version 1.0
Bundle sequencing
Categories Alignment
Authors Gabriele Partel (gabrielepartel@gmail.com)
Issue tracker View/Report issues
Requires boost c++ development libraries. ; R ; R ada package ; Bowtie ; Blat ; faToTwoBit ; BWA ; GMAP ; Seqtk ; Bedtools ; Pysam
Source files component.xml main.sh
Usage Example with default values

Inputs

Name Type Mandatory Description
reads FASTQZ Mandatory Reads in .fq.gz format.
mates FASTQZ Mandatory Mates in .fq.gz format.

Outputs

Name Type Description
out BinaryFolder Output folder. Two special files are added: final a symlink pointing to the final output of the tool, .tool file that tells which tool was used.

Parameters

Name Type Default Description
length string "" read length parameter for SOAPfuse.
sample string (no default) Name of the sample (ID)
threads string "4" Number of threads for parallelization.
tool string "FC" Fusion detection tool used. Possibile values: FC (FusionCatcher), CS (ChimeraScan), DF (deFuse), SF (SOAPfuse), ES (EricScript).

Generated 2018-12-11 07:42:06 by Anduril 2.0.0