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Genomics

How to install Cortex on Ubuntu?

Dr. Muniba Faiza

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Cortex - genome analysis framework

Cortex is a user-friendly framework for genome analysis [1]. It acquires less memory and is quite efficient in performance. It’s installation involves various steps. In this article, we will install Cortex on Ubuntu.

Preparing system

Let’s update and upgrade the system first. Open the terminal (Ctrl+T) and type the following commands:

$ sudo apt-get update

$ sudo apt-get upgrade

Downloading Cortex

Move inside a directory where you want to download the software. Then, paste the following command in your terminal or download it from here.

$ wget https://dl.bintray.com/thehive-project/binary/cortex-latest.zip

Installing Cortex

Extract the zip file using the following command and then install.

$ unzip cortex-latest.zip

It will create a new directory in your current directory, namely, ‘cortex-3.0.1.1′. Now, move inside the new directory and create link.

$ cd cortex-3.0.1-1/

$ ln -s cortex-3.0.1-1 cortex

$ sudo addgroup cortex

$ sudo adduser --system cortex

$ sudo cp /cortex/cortex-3.0.1-1/package/cortex.service /usr/lib/systemd/system

$ sudo chown -R cortex:cortex /cortex/cortex-3.0.1-1/

$ sudo chgrp cortex /cortex/cortex-3.0.1-1/package/cortex.conf

$ sudo chmod 640 /cortex/cortex-3.0.1-1/

$ sudo systemctl enable cortex

$ sudo service cortex start

Now, you can easily run Cortex on your system.


References

  1. Iqbal, Z., Caccamo, M., Turner, I., Flicek, P., & McVean, G. (2012). De novo assembly and genotyping of variants using colored de Bruijn graphs. Nature genetics44(2), 226-232.

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

Genomics

How to Compress and Decompress FASTQ, SAM/BAM & VCF Files using genozip?

Dr. Muniba Faiza

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compressing and decompressing files using genozip

genozip is a tool for lossless compression of large files including VCF, FASTQ, and SAM/BAM files [1]. In this article, we explain the usage of the genozip tool for the compression and decompression of these files. (more…)

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Genomics

Installing BCFtools on Ubuntu

Tariq Abdullah

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Installing bcftools on Ubuntu

BCFtools is a set of utilities that are used to manipulate variant call files (VCF) and binary call files (BCF). It can be used for both compressed and uncompressed sort of files. In this article, we will install BCFtools on Ubuntu. (more…)

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Genomics

Installing CRISPRCasFinder on Ubuntu

Dr. Muniba Faiza

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install crisprcasfinder on ubuntu

CRISPR/Cas9 is a genome editing technology trending fastly. It is used to identify CRISPR associated genes within the genomes of prokaryotic bacterias. Several tools are available for this. Amongst them, CRISPRCasFinder is one that is used to search for CRISPRs and Cas genes in sequence data [1]. In this article, we will install CRISPRCasFinder on Ubuntu. (more…)

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