Banana Slug Genomics

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====== Burrows Wheeler aligner ====== We discussed the [[bioinformatic_tools:bwa]]. It uses the Burrows Wheeler Transform to represent a prefix trie, allowing for short read alignment. ===== The prefix trie ====== 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 ===== Suffix array ====== 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-