Introducing the Trimmomatic

[tonybolger]

I am not able to run trimmomatic on MAC. It gives the error 'Failed to load Main-class manifest attribute from trimmomatic-0.20.jar'.
Is there a way to open this on MAC?
Thanks!

I guess you've tried running it by double-clicking on the jar. Since trimmomatic doesn't have a GUI (yet), this won't work.

You need to run it from the terminal (Applications->Utilities->Terminal), using the command-line parameters as specified on the usadellab.org webpage.

[neethav]

Trimmomatic software problem

I am not able to run trimmomatic on MAC. It gives the error 'Failed to load Main-class manifest attribute from trimmomatic-0.20.jar'.
Is there a way to open this on MAC?
Thanks!

[tonybolger]

A new version (0.2) is now available from the usual place

This version adds multi-threading, which makes it much much faster on multi-core machines, as well as correcting a bug in adapter detection code (which caused it to be overly-aggressive for around ~0.1% of the reads).

[tonybolger]

Keep up the good work - it really is a good tool and so much faster than the others I have tried (still not sure why - but hey, who cares .

Only thing I have been missing - an output log showing how many reads were trimmed, what adapter, etc. That would be really useful.

Thanks for the complements, and glad trimmomatic is working well for you.

There is a trimlog (-trimlog <logfile>), but it currently only summarizes what happened to each read, not why. I agree an 'adapter tracking' log would also be useful.

[kga1978]

Keep up the good work - it really is a good tool and so much faster than the others I have tried (still not sure why - but hey, who cares .

Only thing I have been missing - an output log showing how many reads were trimmed, what adapter, etc. That would be really useful.

[giorgifm]

Dear kg1978,

thanks for using Trimmomatic. We really did put effort in making it fully customizable, fast and memory efficient!

[kga1978]

A bunch - some of them I can't remember as I uninstalled quickly. But I have tried cutadapt, far, btrim, SeqTrim, TagCleaner, prinseq, solexaQA - all nice tools but lacking in features and speed compared to this one (not sure why - but for one file, cutadapt took 3 hours, trimmomatic took 10 min - I almost thought it hadn't worked...).

[pmiguel]

I have recently gone through a bunch of these programs and I gotta say this one is THE best by far - I'm only sorry I didn't find it until now.

Awesome tool - thanks for making it available!

Which other tools did your try?

--
Phillip

[kga1978]

I have recently gone through a bunch of these programs and I gotta say this one is THE best by far - I'm only sorry I didn't find it until now.

Awesome tool - thanks for making it available!

[tonybolger]

Hi All,

I've finally gotten around to making the Trimmomatic, a flexible read-trimming tool for Illumina NGS data available.

Instructions and download link are here. Any questions, requests etc, post 'em.

Since we still have issues getting clearance for including the illumina sequences (hopefully this will be resolved soon), the adapter trimming part won't be usable for now.

Enjoy and happy trimming.