Adapter trimming tool for Windows?

Question

[Amit Lavon]

Hello,

I am looking for an adapter trimming tool for Illumina reads (like cutadapt) that works on Windows, or any alternative tool to cutadapt.

Does anyone know of one?

Thanks,
Amit

[dariober]

Hi- Have you considered installing cygwin and try to use the linux distributions of the various tools? Even better would be to install a possibly lightweight distribution of Linux itself like wubi.

(Sorry, not really an answer to your question...)

[Amit Lavon]

Thanks @dariober. Running Linux is always an option, but I'm trying to keep my work on Windows as much as I can.

[dariober]

Yes, I think i understand... But if you are going to do bioinformatics on a (semi-)regular basis sticking to Windows is going to be more of a hassle than a comfort...

[poisonAlien]

Amount of people trying to install bioinformatic tools on windows is too damn high.

[DareDevil]

I don't recommend ngs data analysis in Windows.

Answer 1

[Dan D]

If you really want to do your adapter trimming in Windows, I'd recommend BBDuk from BBTools.

Otherwise, I'd recommend using Galaxy or Cygwin (as dariober suggested in the comment above).

[Amit Lavon]

Thanks Dan, I'll give it a try.

[Brian Bushnell]

Let me know if you need any help; all of the programs work in Windows, but the shellscripts don't, so the command lines are slightly different and longer than in Linux. e.g.

java -ea -Xmx1g -cp C:\bbmap\current\ jgi.BBDukF in=reads.fq out=trimmed.fq ref=adapters.fa ktrim=r k=25 mink=12

...whereas in Linux the bold part would just be "bbduk.sh".

[Amit Lavon]

Sir, you did some nice work here!

I didn't check the adapter trimming yet, but I ran a benchmark test of BBMap against Bowtie2 on yeast and it had significantly more true positives (though with slightly more false positives). Also, it's cross platform, simple and self descriptive, just the way software should be.

So thumbs up! Keep up the good work. :)

[Brian Bushnell]

I'll do my best =)

You should be able to reduce the false positive rate by filtering on the mapping quality score; BBMap gives lower scores to reads that map to multiple sites similarly well.