Paired-end trimming

[marcelm]

From daniel.k...@gmail.com on September 05, 2012 10:45:42

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: http://code.google.com/p/cutadapt/issues/detail?id=50

[marcelm]

From marcel.m...@tu-dortmund.de on June 11, 2013 02:43:06

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.

[marcelm]

From marcel.m...@tu-dortmund.de on February 06, 2014 14:09:02

Done!

Status: Fixed