TaBSAP ## Targeted Bisulfite Sequencing Analysis Pipeline

User Guide - v1.0.2 A pipeline to analyze the data obtained from targeted bisulfite sequencing through the ion-torrent platform.

TaBSAP is a pipeline to map bisulfite treated sequencing reads to a genome of interest and perform methylation calls in a single step and enables a researcher to analyze the methylation levels of their samples straight away. It’s main features are:

-Bisulfite mapping and methylation calling in one single step

-Supports single-end read alignments

-Alignment seed length, number of mismatches etc. are adjustable

-The output gives heatmap with categories.

Minimum System Requirements

Project Name: TaBS-Pipe

Operating System: 64 bit Unix-like OS/ Linux Distributions(Ubuntu, CentOS, RHEL,etc.),Windows (with cygwin and R in cygwin).

Programming Language: SHELL Scripting.

Other Requirements: R, Pheatmap package for R,fastx toolkit(for 32 bit System ), Dos2Unix.

License: MIT License.


Install the requirements Download the pipeline or clone the Pipeline in your Linux system with git Open Terminal

To download



cd v1.0.2

To Clone

git clone


Copy all the fastq files to fastq folder and Unconverted reference to reference folder Run the pipeline and follow the ON-Screen Instructions ./