Bisulfite Sequencing Processing Platform

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Project description

BSBolt (BiSulfite Bolt)

A fast and safe read alignment platform for bisulfite sequencing data

BiSuflite 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.

Documentation

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

Installation

BSBolt alignment is performed using a modified version of BWA. Read simulation is carried out using a modified version of wgsim.

Install through PIP.

pip3 install BSBolt -v

Install from github.

git clone git@github.com:NuttyLogic/BSBolt.git
cd BSBolt-master
python3 setup.py install .

External Dependencies

BWA-MEM2 and WGSIM forks compiled using gcc 8.3.1 with zlib
Setup.py will fail without gcc and zlib accessible
Bdist Wheels manylinux2010 compatible

Python Dependencies

pysam >= 0.15.4
numpy >=1.16.3
tqdm >= 4.31.1

Project details

These details have not been verified by PyPI

Project links

GitHub Statistics

View statistics for this project via Libraries.io, or by using our public dataset on Google BigQuery

Release history Release notifications | RSS feed

1.6.0

Mar 28, 2023

1.5.0

Feb 14, 2022

1.4.8

Jun 18, 2021

1.4.7

Jun 9, 2021

1.4.6

Jun 8, 2021

1.4.5

Mar 30, 2021

1.4.4

Feb 3, 2021

1.4.1

Jan 27, 2021

1.4.0

Jan 27, 2021

1.3.6

Oct 20, 2020

1.3.5

Oct 5, 2020

1.3.4

Aug 24, 2020

1.3.3

Aug 24, 2020

1.3.2

Aug 24, 2020

1.3.1

Aug 14, 2020

1.3.0

Jul 7, 2020

1.2.3

Jun 25, 2020

1.2.2

Jun 15, 2020

1.2.1

May 26, 2020

1.2.0

May 25, 2020

1.1.2

May 20, 2020

1.1.1

May 19, 2020

1.1.0

May 18, 2020

This version

1.0.0

Apr 9, 2020

0.3.0

Apr 7, 2020

0.1.2

Nov 14, 2019

0.1.1

Oct 8, 2019

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BSBolt-1.0.0.tar.gz (721.9 kB view hashes)

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