I'm preparing a workshop on some introductory topics in bioinformatics and I would like to know which is the best Linux bioinformatics distro.
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written
by
Paulo Nuin
4 answers
The NEBC Bio-Linux distro is rather mature. I think it probably lacks NGS packages, but has a good spread of phylogenetic and general bioinformatics tools (including BLAST and EMBOSS). It was my job developing it several years ago, but it has come a long way since then! It's Ubuntu based and can be run booted off of a USB key. We use it on our Masters course for this kind of work. Full package list is here
I am not sure there is one which does everything bioinformatics-related way better than the others. It all depends on the target audience. With real newbies you may be better off with virtual machines. There is an incomplete list of bioinformatics Linux distros here
Frankly I had no time to test these, so can not vouch for any particular one.
To "do bioinformatics" in general there are several options available, although you may find that they may lack of some things you may need, or that they will have more things than you'll ever need. to be honest, I've never seen a proper bioinformatician looking for a bioinformatics linux distro, but for a flexible one that would allow him/her to easily install and configure all the software packages of his/her interest.
Just in case it helps in any way, all the linux-based bioinformaticians I deal with are mainly based on Fedora and Ubuntu. I personally use the later, because I'm very comfortable with it and allows me to do everything I want, but I'm not a linux guru so that I can suggest any other distro.
PS: I've seen a couple of people with DNALinux as a virtual machine working quite well, although they were using very powerful machines. I wouldn't recommend this if bioinformatics is your main aim, but it can be a solution to do some bioinformatics collaterally to your other needs.
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written
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Jorge Amigo
I'm definitely not looking for a distribution for myself, but looking for something convenient to use in a course/workshop.
You should have a look to Scientific Linux. It is not intentended to do only "bioinformatics", but rather general science, . It has been created to be (as fully as possible) compatible with Red Hat, and it comes with a bunch of interesting packages.
I've been using it for a course and it really deserves a chance.
Cheers,
insectopalo
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Forum: Why Was My Question Deleted?
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Do you already know which tools you are going to use? Then the obvious answer would be, the distro that has the most binary packages of them (especially when the setup it is no longer needed after the workshop).
I should have included more information on the question, but what I'm looking for is something with a nice number of packages (BLast, EMBOSS, some alignment software, maybe NGS) and it's easy to install for some unexperienced users. Most of the people coming to the workshop have Macs which will have their own package, so I need to cover people with Windows-based computers.