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BSBolt (BiSulfite Bolt)

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.

Documentation

BSBolt documentation can be found at bsbolt.readthedocs.io.

Release Notes

  • BSBolt v1.4.5
    • Fixed maximum read depth bug that prevented methylation call on site covered by greater than 8000 reads
    • Refactored build script, with experimental support for M1 Macs
  • BSBolt v1.4.4
    • The default entry point for BSBolt has changed from BSBolt to bsbolt for conda compatibility

Installation

PyPi Installation

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

Conda Installation

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

Dependencies

  • 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

Dependencies

  • autoconf
  • automake
  • homebrew
  • xcode

Installation from source requires xcode command line utilities, homebrew macOS package manager, autoconf, and automake 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/HEAD/install.sh)"
# install autoconf
brew install autoconf
# install automake
brew install automake
# optionally install python
brew install python3.8
# install bsbolt
pip3 install bsbolt