Sequence alignment with BWA

Next, we’ll dive into a core algorithm at the heart of bioinformatics: alignment.Alignment is the process of matching two sequences together so that they share the maximum amount of common sequence, or aligning many reads to a reference sequence. An aligner is any software that specializes in lining up sequencing reads to longer sequences, or in some cases, sets of longer sequences to each other.One of the first core aligners was BWA, the Burrows-Wheeler Aligner (to read more about these aligners, look at the See also section of this recipe).Another important aligner that has been developed recently is the DRAGEN aligner from Illumina. DragMap is an open source version of the DRAGEN aligner.SAMtools (https://www.htslib.org/) is another important program that we’ll be using in this recipe (Li et al., The Sequence Alignment/Map Format and SAMtools, Bioinformatics, June 2009). SAMtools helps us read, write, index, and view SAM and BAM files. It is...