Sunday, February 7, 2016

The Open Metagenome Toolkit Project

Almost two years ago I started collecting some scripts that I wrote for my own microbial metagenomic analyses. These are some relatively simple Perl and Python scripts that do some common tasks that are required when studying bacterial or viral metagenomes. This collection of scripts if called the Open Metagenome Toolkit. I recently added a few more scripts that I think are helpful, including a script to translate nucleotide sequences and a script to calculate the average lengths of reads. This week our post is about the Open Metagenome Toolkit because it is a cool opportunity for collaborative programming in our microbiome community.

Of course I hope you will use this toolkit in your own research because I think it will make your life a little easier. But even more so, I hope you will head over to the Github repository and show off some of your coding skills by contributing some scripts or adding to the scripts that are already there. If you are just getting started with coding, you can use this as a learning opportunity by adding to the existing scripts and getting some feedback.

The point of this project is to facilitate collaboration. With that comes proper credit to every contributor.  Therefore the least we can do is include the names of the contributors on the project homepage, along with a link to their homepage. So go ahead and contribute, and actually be a part of the project no matter what skill level you are at.

In addition to its focus on collaboration, this toolkit focuses on mobility. It relies only on Perl and Python, which are so common that they actually come pre-installed on many operating systems. There is no requirement for installing additional programs or modules, including BioPerl and BioPython. This is a major strength because it means the user does not have to install any dependencies. This is also a nice exercise in programming, and I think offers a high degree of control to the programmer.

So now that you have read the intro, go over and check out the toolkit. It is easy to download, easy to use, and easy to get involved with. If you have any ideas for functions that should be added, go ahead and add them in the issue section. Otherwise you can directly add to the scripts.

Any questions or comments? Let me know in the comments below, on Twitter, or by email. I would love to hear from you!

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