Analysis of large-scale RNA or DNA sequencing data often begins with aligning reads to a reference genome, which is followed by interpretation of the alignment patterns. Alignment is handled by a variety of tools, whose output typically is delivered as a BAM file. The Bioconductor packages Rsamtools and GenomicAlignments provide a flexible interface for importing and manipulating the data in a BAM file, for instance for quality assessment, visualization, event detection and summarization.
