WGT: Tools and algorithms for recognizing, visualizing, and generating Wheeler graphs.

Kuan-Hao Chao, Pei-Wei Chen, Sanjit A Seshia, Ben Langmead

Abstract read

In one paragraph

Article in iScience, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it

0cells of the map it votes in

1citing 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

1 citing paper in PubMed.

GIN-TONIC: non-hierarchical full-text indexing for graph genomes.NAR genomics and bioinformatics · 2024
Article

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

4 authors.

Kuan-Hao ChaoDepartment of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA.

Pei-Wei ChenDepartment of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA 94720, USA.

Sanjit A SeshiaDepartment of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA 94720, USA.

Ben LangmeadDepartment of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA.

Funding

Methods for sequencing data analysis and archive-scale data science - RenewalR35GM139602 · NIGMS · JOHNS HOPKINS UNIVERSITY · PI Benjamin Thomas Langmead · 2021 to 2026

$5.0M

Personal and panel references for improved alignmentR01HG011392 · NHGRI · JOHNS HOPKINS UNIVERSITY · PI LANGMEAD, BENJAMIN THOMAS · 2020 to 2025

$4.2M

NHGRI NIH HHS R01 HG011392NIGMS NIH HHS R35 GM139602

6 · The paper itself

Abstract

A Wheeler graph represents a collection of strings in a way that is particularly easy to index and query. Such a graph is a practical choice for representing a graph-shaped pangenome, and it is the foundation for current graph-based pangenome indexes. However, there are no practical tools to visualize or to check graphs that may have the Wheeler properties. Here, we present Wheelie, an algorithm that combines a

Indexed as

AlgorithmsBioinformaticsData structure

Identifiers

PMID37575187

DOI10.1016/j.isci.2023.107402

PMCPMC10415921

What OpenQuestion holds

Textmetadata

LicenceCC BY

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.