Burrows-Wheeler Transform (BWT) and its FM-index extension are foundational algorithms for highly efficient genomic indexing.

The Burrows-Wheeler Transform (BWT) is a reversible data transformation algorithm that reorders a text into blocks of characters that are similar to each other. This reordering makes the text highly compressible and, crucially for genomics, allows for very fast pattern searching. The FM-index, an extension of the BWT, combines the transformed text with an auxiliary data structure (like suffix arrays) to enable character-by-character searching of a genome without decompressing the entire reference sequence. This approach allows bioinformatics tools like BWA and Bowtie to align millions of short DNA reads against a large reference genome (e.g., human) with remarkable speed and memory efficiency, even on standard computing hardware, making it a cornerstone of modern sequence alignment.