From jkgren...@gmail.com on February 10, 2015 17:22:41

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: http://code.google.com/p/cutadapt/issues/detail?id=97