Package: bsbolt
BSBolt (BiSulfite Bolt)A fast and safe bisulfite sequencing analysis platformBiSuflite Bolt (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 ofBWAandWGSIMfor read alignment and read simulation respectively.
BSBolt is released under the MIT license.PublicationFarrell, C., Thompson, M., Tosevska, A., Oyetunde, A. & Pellegrini, M.BiSulfite Bolt: A BiSulfite Sequencing Analysis Platform.2020.10.06.328559 (2020).
doi:10.1101/2020.10.06.328559DocumentationDocumentation can be found athttps://bsbolt.readthedocs.io.Release Notesv1.6.0MethyDackel compatibilityOption to output alignment to stdoutv1.5.0Improved thread handling for methylation / variant calling.Experimental bisulfite aware SNP caller.v1.4.8Fixed bug ending alignment when the reference template end greater than reference boundary.v1.4.7Alignment stats fix.v1.4.6Alignment statistics now output as generated.Fixed bug where alignment would stop when observed mappability was low.v1.4.5Fixed maximum read depth bug that prevented methylation call on site covered by greater than 8000 readsRefactored build script, with experimental support for M1 Macsv1.4.4The default entry point for BSBolt has changed fromBSBolttobsboltfor conda compatibilityInstallationPyPi InstallationPre-compiled binaries can be installed using PyPi. Binaries are available for python >=3.6
on unix like systems (macOS >=10.15 and linux).pip3installbsbolt--userConda InstallationBSBolt can be installed using the conda package manager using the instructions below.condaconfig--addchannelsbioconda
condaconfig--addchannelsconda-forge
condainstall-ccpfarrellbsboltInstalling from SourceDependencieszlib-devel >= 1.2.3-29GCC >= 8.3.1# clone the repositorygitclonehttps://github.com/NuttyLogic/BSBolt.gitcdbsbolt# compile and install packagepip3install.Installing from Source on macOSDependenciesautoconfautomakehomebrewxcodeInstallation from source requires xcode command line utilities,homebrewmacOS package manager,
autoconf, python (>=3.6), and automake.The full installation process is outlined below.# install xcode utilitiesxcode-select--install# install homebrew/bin/bash-c"$(curl-fsSLhttps://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"# install autoconfbrewinstallautoconf# install automakebrewinstallautomake# optionally install python > 3.5brewinstallpython3.8# clone the repositorygitclonehttps://github.com/NuttyLogic/BSBolt.gitcdBSBolt# compile and install packagepip3install-e.UsageFollowing installation BSBolt can be called usingbsbolt Module.python3-mbsboltbsboltModule

AlignAlignment
IndexIndexGeneration
CallMethylationMethylationCalling
AggregateMatrixCGmapMatrixAggregation
SimulatebsboltIlluminaReadSimulation
ImputekNNImputation
SortSortBAMFile
BamIndexIndexBAMfile