A fast and safe bisulfite sequencing processing platform
BiSuflite Bolt (BSBolt); a fast and scalable bisulfite sequencing processing platform. BSBolt is an integrated analysis platform that offers support for bisulfite sequencing read simulation, alignment, methylation calling, data aggregation, and data imputation. BSBolt has been validated to work with a wide array of bisulfite sequencing data,including whole genome bisulfite sequencing (WGBS), reduced representative bisulfite sequencing data (RRBS), and targeted methylation sequencing data. BSBolt utilizes forked versions of BWA and WGSIM for read alignment and read simulation respectively. BSBolt is released under the MIT license.
BSBolt documentation can be found at bsbolt.readthedocs.io.
- BSBolt v1.4.4
- The default entry point for BSBolt has changed from BSBolt to bsbolt for conda compatibility
Pre-compiled binaries can be installed using PyPi. Binaries are provided for python >=3.6 on unix like systems (macOS >=10.15 and linux).
pip3 install bsbolt --user
BSBolt can be installed using the conda package manager using the installation instructions below.
conda config --add channels bioconda conda config --add channels conda-forge conda install -c cpfarrell bsbolt
Installing from Source
- zlib-devel >= 1.2.3-29
- GCC >= 8.3.1
# clone the repository git clone https://github.com/NuttyLogic/BSBolt.git cd bsbolt # compile and install package pip3 install .
Installing from Source on macOS
Installation from source requires xcode command line utilities, homebrew macOS package manager, and autoconf are installed. Xcode through the mac App Store, running the xcode installation command listed below, or as part of the homebrew macOS package manager installation. The full installation process can be completed as outlined below.
# install xcode utilities xcode-select --install # install homebrew /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install.sh)" # install autoconf brew install autoconf # optionally install python brew install python3.8 # install bsbolt pip3 install bsbolt