Evidence map›Paper›PMID 41497396›Full record

ArticleiScience2025

Run-length compressed metagenomic read classification with SMEM-finding and tagging.

Lore Depuydt, Omar Y Ahmed, Jan Fostier, Ben Langmead, Travis Gagie

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in iScience, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

4 citing papers in PubMed.

  1. Col-BWT: Pangenomic Seed Chaining with Maximal Matches Improves Read Classification.Journal of computational biology : a journal of computational molecular cell biology · 2026
    Article
  2. KeBaB:International Symposium on String Processing and Information Retrieval : SPIRE ... : proceedings. SPIRE (Symposium) · 2026
    Article
  3. Article
  4. An Efficient Data Structure and Algorithm for Long-Match Query in Run-Length Compressed BWT.Algorithms in bioinformatics : ... International Workshop, WABI ..., proceedings. WABI (Workshop) · 2025
    Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

5 authors.

Lore DepuydtDepartment of Information Technology - IDLab, Ghent University - imec, 9052 Gent, Belgium.
Omar Y AhmedDepartment of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA.
Jan FostierDepartment of Information Technology - IDLab, Ghent University - imec, 9052 Gent, Belgium.
Ben LangmeadDepartment of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA.
Travis GagieFaculty of Computer Science, Dalhousie University, Halifax, NS B3H 4R2, Canada.

Funding

Personal and panel references for improved alignmentR01HG011392 · NHGRI · JOHNS HOPKINS UNIVERSITY · PI LANGMEAD, BENJAMIN THOMAS · 2020 to 2025
$4.2M
NHGRI NIH HHS R01 HG011392
6 · The paper itself

Abstract

Metagenomic read classification is a fundamental task in computational biology but remains challenging due to the scale and diversity of sequencing data. We present a run-length compressed BWT-based index using the move structure for efficient multi-class classification. Our method finds all super-maximal exact matches (SMEMs) of length ≥

Indexed as

Biocomputational methodBiological classificationClassification of bioinformatical subjectMicrobial genomics

Identifiers

PMID41497396
PMCPMC12767181

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.