{"doi":"10.1101/gr.277642.123","title":"Efficient taxa identification using a pangenome index","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: <m:math xmlns:m=\"http://www.w3.org/1998/Math/MathML\" display=\"inline\" overflow=\"scroll\"><m:mrow><m:mi mathvariant=\"script\">O</m:mi></m:mrow><m:mo>(</m:mo><m:mi>r</m:mi><m:mo>)</m:mo></m:math> space, where r is the number of Burrows–Wheeler runs. To date, the r -index has lacked the ability to quickly classify matches according to which reference sequences (or sequence groupings, i.e., taxa) a match overlaps. We present new algorithms and methods for solving this problem. Specifically, given a collection D of d documents, <m:math xmlns:m=\"http://www.w3.org/1998/Math/MathML\" display=\"inline\" overflow=\"scroll\"><m:mrow><m:mi mathvariant=\"script\">D</m:mi></m:mrow><m:mo>=</m:mo><m:mo fence=\"false\">{</m:mo><m:mrow><m:msub><m:mi>T</m:mi><m:mn>1</m:mn></m:msub></m:mrow><m:mo>,</m:mo><m:mrow><m:msub><m:mi>T</m:mi><m:mn>2</m:mn></m:msub></m:mrow><m:mo>,</m:mo><m:mo>…</m:mo><m:mo>,</m:mo><m:mrow><m:msub><m:mi>T</m:mi><m:mi>d</m:mi></m:msub></m:mrow><m:mo fence=\"false\">}</m:mo></m:math> over an alphabet of size σ, we extend the r -index with <m:math xmlns:m=\"http://www.w3.org/1998/Math/MathML\" display=\"inline\" overflow=\"scroll\"><m:mrow><m:mi mathvariant=\"script\">O</m:mi></m:mrow><m:mo>(</m:mo><m:mi>r</m:mi><m:mi>d</m:mi><m:mo>)</m:mo></m:math> additional words to support document listing queries for a pattern <m:math xmlns:m=\"http://www.w3.org/1998/Math/MathML\" display=\"inline\" overflow=\"scroll\"><m:mi>S</m:mi><m:mo>[</m:mo><m:mn>1..</m:mn><m:mi>m</m:mi><m:mo>]</m:mo></m:math> that occurs in <m:math xmlns:m=\"http://www.w3.org/1998/Math/MathML\" display=\"inline\" overflow=\"scroll\"><m:mi>n</m:mi><m:mi>d</m:mi><m:mi>o</m:mi><m:mi>c</m:mi></m:math> documents in D in <m:math xmlns:m=\"http://www.w3.org/1998/Math/MathML\" display=\"inline\" overflow=\"scroll\"><m:mrow><m:mi mathvariant=\"script\">O</m:mi></m:mrow><m:mo>(</m:mo><m:mi>m</m:mi><m:mi>log</m:mi><m:mo>⁡</m:mo><m:mrow><m:msub><m:mi>log</m:mi><m:mi>w</m:mi></m:msub></m:mrow><m:mo>(</m:mo><m:mi>σ</m:mi><m:mo>+</m:mo><m:mi>n</m:mi><m:mrow><m:mrow><m:mo>/</m:mo></m:mrow><m:mrow><m:mtext/></m:mrow></m:mrow><m:mi>r</m:mi><m:mo>)</m:mo><m:mo>+</m:mo><m:mi>n</m:mi><m:mi>d</m:mi><m:mi>o</m:mi><m:mi>c</m:mi><m:mo>)</m:mo></m:math> time and <m:math xmlns:m=\"http://www.w3.org/1998/Math/MathML\" display=\"inline\" overflow=\"scroll\"><m:mrow><m:mi mathvariant=\"script\">O</m:mi></m:mrow><m:mo>(</m:mo><m:mi>r</m:mi><m:mi>d</m:mi><m:mo>)</m:mo></m:math> space, where w is the machine word size. Applied in a bacterial mock community experiment, our method is up to three times faster than a comparable method that uses the standard r -index locate queries. We show that our method classifies both simulated and real nanopore reads at the strain level with higher accuracy compared with other approaches. Finally, we present strategies for compacting this structure in applications in which read lengths or match lengths can be bounded.","journal":"Genome Research","year":2023,"id":390065,"datarank":0.40620753016533157,"base_score":2.70805020110221,"endowment":2.70805020110221,"self_citation_contribution":0.40620753016533157,"citation_network_contribution":0.0,"self_endowment_contribution":0.40620753016533157,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":14,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9239,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2023-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":662069,"name":"Massimiliano Rossi","orcid":"0000-0002-3012-1394","position":1,"is_corresponding":false},{"id":321620,"name":"Christina Boucher","orcid":"0000-0001-5617-7495","position":2,"is_corresponding":false},{"id":18148,"name":"Ben Langmead","orcid":"0000-0003-2437-1976","position":3,"is_corresponding":false},{"id":563544,"name":"Omar Ahmed","orcid":"0000-0002-9933-8508","position":0,"is_corresponding":true}],"reference_count":30,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-07-19T01:18:32.854511Z","pmid":"37258301","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}