Filtering/cutting fastq by quality - (Jun/02/2015 )

Fastq includes information about the quality of the sequences. Is there any program that uses this to allow you to cut off the part of the sequence that is low quality? I want to give the fastq to a primer design software without it putting primers on the part of the sequence which may not even be correct. If there is no such program I guess I could try and script it in R or awk or something since it is a plain text format.

Not sure if suitable for your needs but I've been using DynamycTrim (removal of low quality ends by sliding window) and LengthSort (filters out sequences below a certain length, default 25 nt) from the SolexaQA package for the reads coming from Illumina during genome sequencing.