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This analysis workbook will assume that you already have an idea about Next Generation Sequencing and have a general overview of the key stages involved in a data analysis starting with the reads as they come off of the sequencer.  We have devised a simple example workflow comprising the following stages:

You will have the opportunity to map your reads using two different mappers and then compare the outputs.  As we are using simulated data, we have generally applied the default analysis settings for each stage and method.  Working with real life datasets, you should give consideration to the data type you are working with and the experimental objective in order to tune your analysis for optimal results.