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We discussed the bwa. It uses the Burrows Wheeler Transform to represent a prefix trie, allowing for short read alignment.
The prefix trie is a tree built from possible prefixes, starting at the end of a branch and going backwards to the root. Each node is the range in the suffix array where the
The suffix array is found by sorting the cyclic transformation lexicographically and taking their original indices. Range in the suffix array can be found by the R_ and R-