FastQC

FastQC is a quality control analysis tool designed to spot potential problems in high throughput sequencing datasets. Its goal is to provide a simple way by which to check the quality of raw sequence data coming from high throughput sequencing pipelines. It does this by running a modular set of analyses on one or more raw sequence files in fastq or bam format. It then produces a report summarizing the results, and highlighting any areas where the library may appear unusual. This should then direct you to where your data may have problems and allow you to take necessary steps to correct it before doing any further analysis.

FastQC is not tied to any specific type of sequencing technique, so it can be used to look at libraries of various experiment types (Genomic Sequencing, ChIP-Seq, RNA-Seq, BS-Seq etc etc).