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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

Project Homepage:

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

Programming Language: SHELL Scripting.

Recommended System Requirement: 4GB RAM, 64 bit unix/linux OS.

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

License: MIT License.


  1. Install the requirements

  2. 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


  1. Copy all the fastq files to fastq folder and Unconverted reference to reference folder

  2. Run the pipeline and follow the ON-Screen Instructions