Paired-end trimming

[GoogleCodeExporter]

I would like to see paired-end trimming in cutadapt. Input two fastq files 
which are ordered identically, and have all trimming done on both files 
simultaneously. After the trimming of each pair there should be a user-settable 
cutoff to discard the entire pair if one of the reads is shorter than this 
cutoff. 

BWA can't handle out of sync files, and trimmomatic and trim_galore can't 
handle 3' adapters. This functionality in cutadapt would make is 
super-powerful, like batman or ironman. 

cheerio

Daniel

Original issue reported on code.google.com by daniel.k...@gmail.com on 5 Sep 2012 at 8:45

[GoogleCodeExporter]

Some preliminary support for paired-end trimming is available in the 
development version of cutadapt, which you can get via git clone or as a zip 
file 
https://github.com/marcelm/cutadapt/archive/master.zip from Github.

The description of how to use the new --paired-output option, contributed by 
James Casbon, is in the README:
https://github.com/marcelm/cutadapt#paired-end-adapter-trimming .

It's not quite full paired-end support, yet, since it creates temporary files 
and you need to run cutadapt twice, but better than nothing!

Right now it's not quite like Batman, more like Kick-Ass.

Original comment by marcel.m...@tu-dortmund.de on 11 Jun 2013 at 9:43

[GoogleCodeExporter]

Done!

Original comment by marcel.m...@tu-dortmund.de on 6 Feb 2014 at 10:09

• Changed state: Fixed