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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.

Preparing 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

You need to install some packages before installing PANDAseq. Paste the following command in the terminal:

$ sudo apt-get install -y build-essential libtool automake zlib1g-dev libbz2-dev pkg-config

Downloading PANDAseq

Change to the directory where you want to download the software. Let’s say, Downloads. Download the PANDAseq from here or use the following command:

$ cd Downloads/

$ wget https://github.com/neufeld/pandaseq/archive/master.zip

Installing PANDAseq

Unzip the downloaded file using the following command:

$ unzip master.zip

Change to the source directory of PANDAseq,

$ cd pandaseq-master/

Now, install PANDAseq using the following command.

$ ./autogen.sh && ./configure && make && sudo make install

It will take a few minutes to finish. After that, you will be able to run PANDAseq on your system successfully!


References

  1. Masella, A.P., Bartram, A.K., Truszkowski, J.M. et al. (2012). PANDAseq: paired-end assembler for illumina sequences. BMC Bioinformatics 13, 31.

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

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 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. (more…)

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NGS

FiNGS- A New Software providing Filters for Next Generation Sequencing

Tariq Abdullah

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fings

We use somatic variant callers to detect mutations in cancer samples by comparing sequencing data tumor and normal sample pairs. This is followed by some ad-hoc filtering that may produce low precision data resulting in a large number of false positives. (more…)

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