Chimera removal pipeline
Bellerophon is a pipeline created to remove falsely assembled chimeric transcripts in de novo transcriptome assemblies.
The pipeline can be downloaded as a vragrant virtual machine (https://app.vagrantup.com/bellerophon/boxes/bellerophon). This is recommended, as it avoids backwards compatibility problems with TransRate.
To run Bellerophon with Vagrant, download vagrant and virtualbox.
Download the Bellerophon vagrantfile
Run the following command:
vagrant init
When it's done downloading run:
vagrant up
And finally:
vagrant ssh
You are now in the virtual environment to run Bellerophon. Shared data can be found at /vagrant/
You can now run the test run of Bellerophon in the Bellerophon folder:
python Bellerophon.py --assembly Demo.fasta --left All_R1_1000.fastq --right All_R2_1000.fastq --outdir /vagrant/testrun
Note that Bellerophon will make an output directory in the /vagrant/ directory. This is recommended as the disk size of Bellerophon is not large enough for most full transcriptome analyses. It also makes the results of the analysis available on the host system, rather than only on the virtual machine.
Bellerophon can also be installed locally. This is the preferred option for users without root permission and Vagrant, but with access to Conda. The easies way for local installation is the use of Conda. After cloning this repository, run the following command to create the conda environment:
conda env create envs/Bellerophon.yml
After installation, run the following command to activate the conda environment:
conda activate Bellerophon
- Custom order of filtering steps is disabled in this version
- This document needs to be expanded