Christina Boucher

May 30, 2024 | biorxiv.org | Omar Ahmed |Christina Boucher |Ben Langmead |Johns Hopkins

AbstractTaxonomic sequence classification is a computational problem central to the study of metagenomics and evolution. Advances in compressed indexing with the r-index enable full-text pattern matching against large sequence collections. But the data structures that link pattern sequences to their clades of origin still do not scale well to large collections.

May 31, 2023 | genome.cshlp.org | Omar Ahmed |Massimiliano Rossi |Christina Boucher |Ben Langmead

↵* Corresponding author; email: omaryfekry{at}gmail.com Abstract Tools that classify sequencing reads against a database of reference sequences require efficient index data structures. The r-index is a compressed full-text index that answers substring presence/absence, count and locate queries in space proportional to the amount of distinct sequence in the database: O(r) space where r is the number of Burrows-Wheeler runs.