This is a python implementation of the Burrows Wheeler Alignment for DNA sequence matching. I wrote this to better understand the BWA algorithm, and to practice my Python skills. I recommend reading up about this algorithm before diving into the implementation below.

• It does not implement any of the heuristic methods included in the actual BWA algorithm, so implements the basic algorithm which returns 100% accurate results
• It uses the Burrows-Wheeler transform (BWT), Suffix Array (SA), and 2 other auxillary datastructures C and Occ (sometimes called O)
• It uses the D array to prune the tree search and speed up the inexact search algorithm.
• The search is case insensitive.

• This is not in any way optimised. This has been coded for ease of understanding, ease of reading and with the goal of better understaning the basic BWA algorithm and its datastructures
• This code parses the suffix tree using a recursive depth-first search, while the real BWA uses breadth-first search (and a heap datastructure), and uses this to prioritise the best partial alignments first
• If BWA finds a result with a difference score of z, it only further considers matches with difference z+1, speeding up the process by ignoring worse results and pruning the search space more aggresively
• BWA sets a maximum allowed difference in the first few tens of bases (called the seed) resulting in 2.5x improvement, and very little loss in accuracy. This is not effective on shorter reads (<50bp)
• BWA reduces the required operating memory by storing small fractions of the Occ and SA arrays, and calculating the rest on the fly. This implementation does not do this.