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
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
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".
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. :)
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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...)
Thanks @dariober. Running Linux is always an option, but I'm trying to keep my work on Windows as much as I can.
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...
Amount of people trying to install bioinformatic tools on windows is too damn high.
I don't recommend
ngs data analysis
in Windows.