An important step in next generation sequencing is the alignment (mapping) of the short reads that are generated to a reference genome. Tools designed for mapping are required to efficiently and accurately align each read and more than 60 applications are currently available for this purpose. In this presentation I will describe some of the approaches to sequence alignment, highlighting popular tools that are used such as BWA, Novoalign and Bowtie. An important consideration for mapping and downstream sequence analysis is the ability to recognise and deal with common errors and biases that can occur during the process. I will discuss some of the common errors that occur in next generation sequencing and the approaches to quality control that should be applied in order to obtain high quality data.