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        "author": "Colin P. Farrell",
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        "description": "# **BSBolt (BiSulfite Bolt)**\n\n## A fast and safe bisulfite sequencing analysis platform\n\n[BiSuflite Bolt (BSBolt)](https://github.com/NuttyLogic/BSBolt); a fast and scalable bisulfite sequencing\nanalysis platform. BSBolt is an integrated analysis platform that offers support for bisulfite sequencing\nread simulation, alignment, methylation calling, data aggregation, and data imputation. BSBolt has been validated\nto work with a wide array of bisulfite sequencing data,including whole genome bisulfite sequencing (WGBS),\nreduced representative bisulfite sequencing data (RRBS), and targeted methylation sequencing data.\nBSBolt utilizes forked versions of [BWA](https://github.com/lh3/bwa)\nand [WGSIM](https://github.com/lh3/wgsim) for read alignment and read simulation respectively.\nBSBolt is released under the MIT license.\n\n## Publication\n\n[Farrell, C., Thompson, M., Tosevska, A., Oyetunde, A. & Pellegrini, M. \n**BiSulfite Bolt: A BiSulfite Sequencing Analysis Platform.** 2020.10.06.328559 (2020). \ndoi:10.1101/2020.10.06.328559](https://academic.oup.com/gigascience/article/10/5/giab033/6272610)\n\n## Documentation\n\nDocumentation can be found at [https://bsbolt.readthedocs.io](https://bsbolt.readthedocs.io/en/latest/).\n\n## Release Notes\n- v1.5.0\n  - Improved thread handling for methylation / variant calling.\n  - Experimental bisulfite aware SNP caller. \n- v1.4.8\n  - Fixed bug ending alignment when the reference template end greater than reference boundary.\n- v1.4.7\n  - Alignment stats fix.\n- v1.4.6\n  - Alignment statistics now output as generated.\n  - Fixed bug where alignment would stop when observed mappability was low.\n- v1.4.5\n  - Fixed maximum read depth bug that prevented methylation call on site covered by greater than 8000 reads\n  - Refactored build script, with experimental support for M1 Macs\n- v1.4.4\n  - The default entry point for BSBolt has changed from **BSBolt** to **bsbolt** for conda compatibility\n\n## **Installation**\n\n### **PyPi Installation**\n\nPre-compiled binaries can be installed using PyPi. Binaries are available for python >=3.6\non unix like systems (macOS >=10.15 and linux).\n\n```shell\npip3 install bsbolt --user\n```\n\n### **Conda Installation**\n\nBSBolt can be installed using the conda package manager using the instructions below.\n\n```shell\nconda config --add channels bioconda\nconda config --add channels conda-forge\nconda install -c cpfarrell bsbolt\n```\n\n### **Installing from Source**\n\nDependencies\n\n* zlib-devel >= 1.2.3-29\n* GCC >= 8.3.1\n\n```shell\n# clone the repository\ngit clone https://github.com/NuttyLogic/BSBolt.git\ncd bsbolt\n# compile and install package\npip3 install .\n```\n\n### **Installing from Source on macOS**\n\nDependencies \n\n- autoconf\n- automake\n- homebrew\n- xcode\n\nInstallation from source requires xcode command line utilities, [homebrew](https://brew.sh/) macOS package manager, \nautoconf, python (>=3.6), and automake.The full installation process is outlined below.\n\n```shell\n# install xcode utilities\nxcode-select --install\n# install homebrew\n/bin/bash -c \"$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)\"\n# install autoconf\nbrew install autoconf\n# install automake\nbrew install automake\n# optionally install python > 3.5\nbrew install python3.8\n# clone the repository\ngit clone https://github.com/NuttyLogic/BSBolt.git\ncd BSBolt\n# compile and install package\npip3 install -e .\n```\n## Usage\n\nFollowing installation BSBolt can be called using **bsbolt Module**.\n\n```shell\npython3 -m bsbolt\n```\n\n```shell\nbsbolt Module\n\nAlign               Alignment\nIndex               Index Generation\nCallMethylation     Methylation Calling\nAggregateMatrix     CGmap Matrix Aggregation\nSimulate            bsbolt Illumina Read Simulation\nImpute              kNN Imputation\nSort                Sort BAM File\nBamIndex            Index BAM file\n```\n\n\n",
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