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bwt_fmindex's Introduction

bwt_fmindex

Burrows–Wheeler Transform and basic FM indexing. Writing these was a learning tool to understand the underlying processes in DNA alignment in tools such as BWA or Bowtie

bwt.py

bwt_encode function using indices and a suffix array, avoiding in-memory sorting of all rotations bwt_decode function using LF mapping

fmindex.py

a simple implementation of FM indexing to do substring queries. Practical use would necessitate compression of encoded string, using a more sparcely calculated Occ table, and improving the algorythm for translating the FM index back into text index.

sources: Ferragina, Paolo & Manzini, Giovanni. (2000). Opportunistic Data Structures with Applications.

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