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Installing Bismark on Ubuntu

Dr. Muniba Faiza

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Installing Bismark on Ubuntu

Bismark is a bioinformatics tool to map bisulfite treated sequencing reads to a genome [1]. It also determines cytosine methylation sites. In this article, we will install Bismark on Ubuntu.

Preparing the system

Open a terminal by pressing Ctrl+Alt+T. Update and upgrade your system using the following commands:

$ sudo apt-get update

$ sudo apt-get upgrade

Installing pre-requisites

To install Bismark, you need to download and install two other software: Bowtie2 and Samtools. So, let’s install them first as shown below.

Installing Bowtie2

$ sudo apt-get install -y bowtie2

Installing Samtools

Change to a directory where you want to download the software, let’s say, Downloads. Now, download Samtools using the following command:

$ cd Downloads/

$ wget https://github.com/samtools/samtools/releases/download/1.10/samtools-1.10.tar.bz2

Extract the file and install using the following commands:

$ tar xjf samtools-1.10.tar.bz2

$ cd samtools-1.10/

$ ./configure

$ make

$ sudo make install

Now check it by typing $ samtools in the terminal. After successful installation, it should display its usage.

Now let’s move to the installation of the Bismark package.

Downloading Bismark

Now, let’s move back to the Downloads directory and download the Bismark software.

$ cd ../

$ wget https://github.com/FelixKrueger/Bismark/archive/master.zip

Now, unzip the file.

$ unzip master.zip

It will create a new directory in Downloads, namely, Bismark-master. It contains all the executable files. You can also check the installation by typing $ bismark, it should display the usage.

That’s all for the installation of Bismark on Ubuntu.


References

  1. Krueger, F., & Andrews, S. R. (2011). Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. bioinformatics27(11), 1571-1572.

Dr. Muniba is a Bioinformatician based in New Delhi, India. She has completed her PhD in Bioinformatics from South China University of Technology, Guangzhou, China. She has cutting edge knowledge of bioinformatics tools, algorithms, and drug designing. When she is not reading she is found enjoying with the family. Know more about Muniba

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[Tutorial] Trailing of paired end reads using Trimmomatic tool in GALAXY.

Dr. Muniba Faiza

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How to generate config file for docking using Autodock Tools?

Trimmomatic is a read trimming tool for Illumina NGS data [1]. It is a flexible tool providing several functions to be operated on reads. These functions include trailing, leading, and several other quality control operations. In this article, we are going to perform trailing on NGS paired-end reads data using the GALAXY platform [2]. (more…)

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NGS

How to extract methylation call using Bismark?

Dr. Muniba Faiza

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How to extract methylation call using Bismark?

Bismark is bioinformatics to map bisulfite treated sequencing reads and to perform methylation calls [1]. In this article, we are going to extract methylation information from Bismark alignment outputs. (more…)

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NGS

Installing PANDAseq on Ubuntu

Dr. Muniba Faiza

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Installing pandaseq on Ubuntu

PANDAseq is a bioinformatics tool that aligns paired-ends of Illumina sequences [1]. In this article, we are going to install PANDAseq on Ubuntu. (more…)

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