Rik is correct, seqfilter will filter out entire reads from a FASTQ file, whereas seqtrim modifies the sequences themselves. seqtrim is needed because reads typically have lower quality at the termini, which can lead to poor or incorrect alignment. However, even after trimming reads, many reads may not contain enough high-quality bases to be included in an analysis, and must be filtered out.
A typical QC pipeline will need to do both to produce high-quality reads before alignment. seqqcplot can be a helpful tool to analyze your reads to determine what preprocessing is appropriate for your application.
