R Bioinformatics Cookbook

Visualizing the quality control of read-to-reference alignments

Once the alignment of reads has been performed, it is usually wise to check the quality of the alignment and ensure that there is nothing unexpected about the pattern of reads and things such as expected insert distances. This can be especially useful in draft reference genomes where unusual alignments of high-throughput reads can reveal misassemblies of the reference or other structural rearrangements. In this recipe, we'll use a package called ramwas, which has some easily accessed plots we can create to assess alignment.