A bioinformatics toolkit for processing high-throughput lymphocyte receptor sequencing data.
Project description
pRESTO is a toolkit for processing raw reads from high-throughput sequencing of lymphocyte repertoires. Dramatic improvements in high-throughput sequencing technologies now enable large-scale characterization of immunoglobulin repertoires, defined as the collection of trans-membrane antigen-receptor proteins located on the surface of T and B lymphocytes. The REpertoire Sequencing TOolkit (pRESTO) is composed of a suite of utilities to handle all stages of sequence processing prior to germline segment assignment. pRESTO is designed to handle either single reads or paired-end reads. It includes features for quality control, primer masking, annotation of reads with sequence embedded barcodes, generation of single-molecule consensus sequences, assembly of paired-end reads and identification of duplicate sequences. Numerous options for sequence sorting, sampling and conversion operations are also included.
Requirements
Installation - Linux
The simplest way to install all Python dependencies is to install the full SciPy stack using the instructions, then install Biopython according to its instructions.
- Extract the pRESTO bundle and run:> python3 setup.py install --user
Installation - Windows
Install Python 3.4.0+ from Python, selecting both the options ‘pip’ and ‘Add python.exe to Path’.
Install NumPy, SciPy, pandas and Biopython using the packages available from the Unofficial Windows binary collection.
- Unzip the pRESTO bundle, open a Command Prompt, change directories to the pRESTO folder, and run:> python setup.py install.
For a default installation of Python 3.4, the pRESTO scripts will be installed into C:\Python34\Scripts and should be directly executable from the Command Prompt. If this is not the case, then follow step 5 below.
Add both the C:\Python34 and C:\Python34\Scripts directories to your %Path%. On Windows 7 the %Path% setting is located under Control Panel -> System and Security -> System -> Advanced System Settings -> Environment variables -> System variables -> Path.
Installation - Mac OS X
Install Xcode 3.2.6 Available from the Apple store or developer downloads. If you have a newer version (eg, Xcode 4.6.3) that will work also, but Xcode 3 is free of charge. If Xcode fails to install with an “Unknown Error”, change the date on your system to some time in 2011, install Xcode, and then change the date back to the proper setting.
Install XQuartz 2.7.5 Available from the XQuartz project.
Install Homebrew Follow the installation and post-installation instructions.
- Open a terminal and install gfortran (required for SciPy) using Homebrew (this can take an hour to install):> brew install gfortranIf the above fails run this instead:> brew install --env=std gfortran
- Install Python 3.4.0+ and set the path to the python3 executable:> brew install python3> echo 'export PATH=/usr/local/bin:$PATH' >> ~/.profileExit and reopen the terminal application so the PATH setting takes effect
- Install NumPy, SciPy, pandas and Biopyton using the Python package manager:> pip3 install numpy scipy pandas biopython
- Extract the pRESTO bundle, open a terminal window, change directories to the pRESTO folder, and run:> python3 setup.py install
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