To assess sequence data quality, try using the FASTQC application. Provides you with an html report detailling multiple sequence statistics on the fastq file.
Extra side-note: it can be a little hard to look through a gajillion FastQC output files for sample specific issues- you can use MultiQC (http://multiqc.info/) to combine all the output files into one condensed report.
just tried out multiqc and yes its is a great tool if you have multiple samples to look at QC. Tks Jeff.