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Radha Agarkar

Radha Agarkar

A Bioinformatician

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Question: Question: Is Linux OS necessary for Bioinformatics? If yes which one is the best for NGS analysis.

Radha Agarkar

Radha Agarkar
3859 days ago
Question: Is Linux OS necessary for Bioinformatics? If yes which one is the best for NGS analysis.

I am currently working on NGS, and looking for a nice OS to handle huge amount of genomics data with an ease. Someone suggested me that Window OS will be a bad idea to use for NGS analysis. I need your valuable suggestion for the best.

Thanks
Answers
1

Hello Radha,

In the Bioinformatics Linux and Unix is recommended. because

  1. Most of High performance Software for Bioinformatics can developed for Linux.
  2. Linux is Faster then Windows because Windows can not able to use your Computer RAM more  then 4GB but Linux can use unlimited.its make you process faster.
  3. Linux is very secure OS compare to Windows. your all data keep secure in Linux OS.
  4. For the Next Generation Analysis you need high speed sequence analysis. so u have to use Linux.it's does not matter which Linux OS you can use for NGS. because all the Linux Software can work in any Linux OS.
  5. If you want to use Linux OS then i suggested you UBUNTU 12.04 LTS. UBUNTU is very simple and user friendly environment and its easy to use and faster operating system. UBUNTU is freely available u dont have to pay for it and its long time supported OS. u can also able to use UBUNTU and Windows at the time by installing GRAB dual boot.

Thank you.

RAJESH DETROJA
RAJESH DETROJA 3859 days ago


1

Hi Radha,

Go for Linux. It's the first citizen for every C, C++, Python, Perl and Ruby Pipeline.

As for the Linux distribution, Try Gentto ( http://www.gentoo.org/ ) for best perfomance or BioLinux ( http://en.wikipedia.org/wiki/BioLinux ) for simple use. You might also look into CentOS, which is an Enterprise-class Linux Distribution derived from sources freely provided to the public by RedHat (as Rohan suggested to consider). In other words it is build on the source code from RedHat and it is free (see http://www.centos.org. It might be of advantage to use CentOS (if you don't want to spend money) since most of the commercial software is certified to run on RedHat and CentOS is 100% binary compatible to it. Moreover, If you planing to build a computing cluster then I suggest you to look into Rocks-cluster (http://www.rocksclusters.org) which is based on CentOS Linux. It is very easy to setup and to maintain.

For a novice linux user, I will recommend BioLinux, which is user-friendly and have pre-installed bioinformatics softwares. Bio-Linux 7 is a fully featured, powerful, configurable and easy to maintain bioinformatics workstation.Bio-Linux provides more than 500 bioinformatics programs on an Ubuntu Linux 12.04 LTS base. There is a graphical menu for bioinformatics programs, as well as easy access to the Bio-Linux bioinformatics documentation system and sample data useful for testing programs. http://nebc.nerc.ac.uk/tools/bio-linux/bio-linux-7-info

Thanks

 

Jit
Jit 3859 days ago


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