option to remove reads that fail the Casava filter

[GoogleCodeExporter]

Hi,
I use cutadapt to trim Illumina reads for adaptor sequences and low-quality 
bases. I would love to also have the option to filter out reads that fail the 
Casava 1.8 filter ("Y" in sequence id line) since the fastq files I receive 
contain failed reads.
Thanks for considering this (easy) filter,
Jen

Original issue reported on code.google.com by jkgren...@gmail.com on 10 Feb 2015 at 4:22

[GoogleCodeExporter]

Give me a few days to think about this. Sure, it’s easy to implement, but it 
does not have to do anything with adapter trimming per se. But then quality 
trimming, which cutadapt also does, is also not really adapter trimming ...

Original comment by marcel.m...@tu-dortmund.de on 11 Feb 2015 at 1:17

[GoogleCodeExporter]

Thanks for considering. I like to use cutadapt as a high quality, tunable 
one-stop-shop for preprocessing, including adaptor trimming, quality trimming, 
length filtering (post-trim), and (ideally) Casava-filtering. Saves me time not 
to have to do each step separately, since I/O is the slow part!

Original comment by jkgren...@gmail.com on 11 Feb 2015 at 2:20

[GoogleCodeExporter]

I understand because that’s how I like to use cutadapt myself ;-). However, 
disk I/O shouldn’t be an issue even if you use multiple programs since you 
can use a pipe to connect them together, similar to this:

   my-casava-filter-program input.fastq | cutadapt -a ADAPTER - > output.fastq

(Assuming here that my-casava-filter-program writes the reads to standard 
output.)

Original comment by marcel.m...@tu-dortmund.de on 11 Feb 2015 at 2:54

[GoogleCodeExporter]

True! But there arent any (good) Casava-filtering programs out there (that
I could find). I wrote a quick awk script but Im not really a programmer.
Imight also have to pipe through gzip (twice) to handle the fastq file
de/compression.
Anyway, thanks for considering, its certainly true there are other options!

Original comment by jkgren...@gmail.com on 11 Feb 2015 at 3:39