Suffix Arrays, Suffix Trees, the Burrows-Wheeler Transform and the FM Index

Deep End Era. Engineering with Sankalp · Oct 28, 2026 · 51m

A fictional Nairobi genomics lab places 300 million reads to find one changed letter. Worked by ear on "banana": the suffix array, prefix doubling, the longest repeat, the BWT and its inversion, and an FM-index backward search. Plus medieval concordances, David Wheeler's career, pseudogene traps, reference genome politics, and when not to build an index.

Chapters

00:00:00 Cold open: three hundred million needles

00:02:41 Searching the text, not the pattern

00:04:08 Suffix trees

00:06:52 A very old idea: the concordance

00:08:47 An analogy for the suffix array

00:10:06 Suffix arrays: just sort…