Install trimmomatic on windows computer?

Question

[pms]

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

[GenoMax]

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.

[cschu181]

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.

[cschu181]

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.

[pms]

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!!!

[pms]

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

[GenoMax]

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

[fishgolden]

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)

[Gio12]

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.

[cpad0112]

try miniconda on windows https://conda.io/en/latest/miniconda.html paula.morenosanz

[pms]

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

[Ram]

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.

Answer 1

[h.mon]

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.

[pms]

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!

[jared.andrews07]

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.

Answer 2

[sethadam30]

Yes, you can use Trimmomatic in WIndows.

1. dl and install JRE https://java.com/en/download/win10.jsp
2. dl binary Trimmomattic v0.39 from http://www.usadellab.org/cms/?page=trimmomatic
3. Unzip the whole Trimmomatic folder to a destination (e.g., desktop)
4. Right click on .jar file in Trimmomatic folder, under Properties --> General change the application which opens .jar to "Java SE" Alternately, right click on the .jar and go to "open with" and select Java SE
5. Create a new text file in the Trimmomatic folder. Rename it run.bat (ensure the extension is .bat not .txt after save).
6. Open the run.bat file in a text editor like Notepad and change to the shell type command that you would use in Linux (e.g. java -jar trimmomatic-0.39.jar SE -phred33 input_file_name.fastq output_file_name.fastq MINLEN:50).

Note, if you drop the new file into the Trimmomatic folder no path is needed, just file names

[sethadam30]

And to run Program, double click the run.bat file. You will need to change and update the run.bat file each time you have a fastq file.

[Ram]

You will need to change and update the run.bat file each time you have a fastq file

That is bad (bordering on horrible) advice. Users should run the command directly and make changes in the command they run, not edit a batch script and execute the edited batch script. You should be advising people to run

java -jar /path/to/trimmomatic.jar <options>

not hardcode a command in a batch file and edit+double click the batch file each time.

Also, this is the solution recommended by h.mon as well. Your "answer" should have been a comment on h.mon's answer as it is just a step-by-step guide to execute that answer.