NB! For the latest version of this pipeline go to: AfshinLab/BLR

Barcode-Linked Reads Analysis

Content:

Usage
One-time installation
Old version

Usage

1. Setup an analysis folder

Activate your Conda environment.

conda activate blr

Choose a name for the analysis. It will be output_folder in this example. Create the analysis directory.

blr init --reads1=path/to/sample.R1.fastq.gz path/to/output_folder

Note that BLR expects paired-end reads. However, only the path to the R1 file needs to be provided. The R2 file will be found automatically.

To use the other blr commands, make sure you working directory is your newly created analysis folder.

cd path/to/output_folder

Then, you may need to edit the configuration file blr.yaml, in particular to enter the path to your reference genome.

blr set --genome_reference=path/to/GRCh38.fasta

To see what other configurations can be altered, read the documentation in the blr.yaml file.

2. Running an analysis

Change working directory to your analysis folder

cd path/to/output_folder

The pipeline automatically runs all steps.

blr run

For more options, see the documentation.

blr run -h

One-time installation

1. Prerequisite: Conda

Install miniconda
Enable the bioconda channel

You could also try copy-pasting the following to your terminal. This will download miniconda, install it to you $HOME folder and enable the bioconda channel.

if [[ $OSTYPE = "linux-gnu" ]]; then 
    wget http://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
elif [[ $OSTYPE = "darwin"* ]]; then 
    wget https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -O miniconda.sh
fi
bash miniconda.sh -b -p $HOME/miniconda
source $HOME/miniconda/etc/profile.d/conda.sh
conda config --add channels bioconda

2. Install

Clone the git repository.

  git clone https://github.com/FrickTobias/BLR.git

Create & activate a new Conda environment, in which all dependencies will be installed.

  conda env create -n blr -f environment.yml
  conda activate blr

Install blr into the environment in "editable install" mode.

  pip install -e .

This will install blr in such a way that you can still modify the source code and get any changes immediately without re-installing.

2.1 Linux users (not macOS)

To enable DeepVariant, install it separately to your environment.

conda activate blr
conda install deepvariant

This will enable the variant_caller: deepvariant option in the analysis config file.

3. Updating

Change working directory to your blr git folder and update.

cd path/to/BLR
git pull

Old version

To run the analysis described in High throughput barcoding method for genome-scale phasing, look at the stable branch for this git repository.

That version of BLR Analysis is also available at OMICtools.

FrickTobias / BLR

readme