BAMStats: summarising Next Generation Sequencing alignments

http://bamstats.sourceforge.net/

Mapping is a prerequisite for most next generation sequencing workflows and the SAM/BAM file format (1) is the de facto standard for storing such large sequence alignments. BAMStats, is a simple software tool built on the Picard Java API (2), which  can calculate and graphically display various metrics derived from SAM/BAM files of value in QC assessments.