Metadata-Version: 2.1
Name: bsbolt
Version: 1.4.8
Summary: Bisulfite Sequencing Processing Platform
Home-page: https://github.com/NuttyLogic/BSBolt
Author: Colin P. Farrell
Author-email: colinpfarrell@gmail.com
License: MIT
Project-URL: Documentation, https://bsbolt.readthedocs.io/en/latest/
Description: # **BSBolt (BiSulfite Bolt)**
        
        ## A fast and safe bisulfite sequencing analysis platform
        
        [BiSuflite Bolt (BSBolt)](https://github.com/NuttyLogic/BSBolt); a fast and scalable bisulfite sequencing
        analysis 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](https://github.com/lh3/bwa)
        and [WGSIM](https://github.com/lh3/wgsim) for read alignment and read simulation respectively.
        BSBolt is released under the MIT license.
        
        ## Publication
        
        [Farrell, C., Thompson, M., Tosevska, A., Oyetunde, A. & Pellegrini, M. 
        **BiSulfite Bolt: A BiSulfite Sequencing Analysis Platform.** 2020.10.06.328559 (2020). 
        doi:10.1101/2020.10.06.328559](https://academic.oup.com/gigascience/article/10/5/giab033/6272610)
        
        ## Release Notes
        - v1.4.8
          - Fixed bug ending alignment when the reference template end greater than reference boundary.
        - v1.4.7
          - Alignment stats fix. 
        - v1.4.6
          - Alignment statistics now output as generated. 
          - Fixed bug where alignment would stop when observed mappability was low.
        - 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
        - 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 available for python >=3.6
        on unix like systems (macOS >=10.15 and linux).
        
        ```shell
        pip3 install bsbolt --user
        ```
        
        ### **Conda Installation**
        
        BSBolt can be installed using the conda package manager using the instructions below. 
        
        ```shell
        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
        
        ```shell
        # 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](https://brew.sh/) macOS package manager, 
        autoconf, python (>=3.6), and automake.The full installation process is outlined below.
        
        ```shell
        # 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 installa automake
        # optionally install python > 3.5
        brew install python3.8
        # clone the repository
        git clone https://github.com/NuttyLogic/BSBolt.git
        cd bsbolt
        # compile and install package
        pip3 install .
        ```
        ## Usage
        
        Following installation BSBolt can be called using **bsbolt Module**.
        
        ```shell
        python3 -m bsbolt
        ```
        
        ```shell
        bsbolt Module
        
        Align               Alignment
        Index               Index Generation
        CallMethylation     Methylation Calling
        AggregateMatrix     CGmap Matrix Aggregation
        Simulate            bsbolt Illumina Read Simulation
        Impute              kNN Imputation
        Sort                Sort BAM File
        BamIndex            Index BAM file
        ```
        
        
        
        
Platform: Linux
Platform: Mac OS-X
Platform: Unix
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Requires: pysam
Requires: numpy
Requires: tqdm
Requires-Python: >=3.6
Description-Content-Type: text/markdown
