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Install trimmomatic on windows computer?
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13 months ago
pms • 0

Hello, I wanted to know if trimmomatic can only be run on GNU GPL v3 or it can also be run on windows environment? I am new to bioinformatics and I have no much knowledge of basic informatics neither.... I need to trim fastq files. Thanks, PMS

sequencing • 509 views
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BBMap suite is Java based and will work on Windows. It has a program called "bbduk" that will do trimming.

That said you should really go the unix route if you can. You are bound to run into some other limitation real quick on Windows since most software for NGS data analysis runs on unix.

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Trimmomatic is java-based as well. :P There's a good reason to not advertise using bioinformatics tools on windows, though... It saves us all a lot of pain in the long run.

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You could install cygwin and then try running it from there. Or try virtual box. Just as a side note, GNU GPL v3 is a license, not an operating system.

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Thank you very much! Well.. as you see ("GNU GPL is not an operating system, it is a software license - by the way, Trimmomatic in licensed under the GNU GPL v3.") my knowledge on informatics is 0.... I think I will try the virtual box. Thank you!!!

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and in MAC, I mean IOS system (right?). Would it work?

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It should work on macOS (not iOS so not on iPad etc). macOS is BSD-unix like operating system.

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I could run trimmomatic with windows 10 Home +

openjdk version "1.8.0_192"

OpenJDK Runtime Environment (build 1.8.0_192-amazon-corretto-preview2-b12)

OpenJDK 64-Bit Server VM (build 25.192-b12, mixed mode)

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If you want to skip the installation procedure, you can make a free account in Galaxy, which has Trimmomatic and several other bioinformatic tools available. It is a great start if you are new to bioinformatics.

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Thank you all for your useful comments!!!! I will let you know my progresses...... :p

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Please do not add an answer unless you're answering the top-level question. Also, please avoid emoji like the tongue-out (:p) in a professional setting.

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11 months ago
h.mon 25k
Brazil

Trimmomatic is a Java application, and probably can be run on windows (see, for example, this discussion at Introducing the Trimmomatic). However, you will find few (if any) help around if you encounter problems. I would advise you to use Linux, or install the Windows Subsystem for Linux, in case you are using Windows 10.

GNU GPL is not an operating system, it is a software license - by the way, Trimmomatic is licensed under the GNU GPL v3.

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with " ...probably can be run on windows " you mean that then the commands that I would have to write would be very different from that shown on http://www.usadellab.org/cms/index.php?page=trimmomatic This will be a challenge for me.....

Thank you for your suggestions!

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The commands to the program would be the same, it just might be slightly different to install. However, if you use the Windows Subsystem for Linux, you can just follow the linux install instructions and get familiar with the best platform for general bioinformatics on a Windows machine.

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