Evidence map›Paper›PMID 40297742›Full record

ArticleAlgorithms in bioinformatics : ... International Workshop, WABI ..., proceedings. WABI (Workshop)2024

Applying the Safe-And-Complete Framework to Practical Genome Assembly.

Sebastian Schmidt, Santeri Toivonen, Paul Medvedev, Alexandru I Tomescu

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Algorithms in bioinformatics : ... International Workshop, WABI ..., proceedings. WABI (Workshop), 2024. 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. Article
  2. Review
  3. High-resolution metagenome assembly for modern long reads with myloasm.bioRxiv : the preprint server for biology · 2025
    Article
  4. 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.

Sebastian SchmidtDepartment of Computer Science, University of Helsinki, Finland.ORCID 0000-0003-4878-2809
Santeri ToivonenDepartment of Computer Science, University of Helsinki, Finland.
Paul MedvedevDepartment of Computer Science and Engineering, The Pennsylvania State University, University Park, PA, USA.
Alexandru I TomescuDepartment of Computer Science, University of Helsinki, Finland.ORCID 0000-0002-5747-8350

Funding

Leveraging k-mer sketching statistics to enhance metagenomic methods and alignment algorithmsR01GM146462 · NIGMS · PENNSYLVANIA STATE UNIVERSITY, THE · PI Antonio Blanca Pimentel, David Koslicki · 2022 to 2026
$2.2M
NIGMS NIH HHS R01 GM146462
6 · The paper itself

Abstract

Despite the long history of genome assembly research, there remains a large gap between the theoretical and practical work. There is practical software with little theoretical underpinning of accuracy on one hand and theoretical algorithms which have not been adopted in practice on the other. In this paper we attempt to bridge the gap between theory and practice by showing how the theoretical safe-and-complete framework can be integrated into existing assemblers in order to improve contiguity. The optimal algorithm in this framework, called the

Indexed as

Applied computing → Computational biologyAssembly evaluationGenome assemblygraph algorithmHiFi sequencing dataMathematics of computing → Paths and connectivity problemsOmnitigsSafe-and-complete frameworkTheory of computation → Graph algorithms analysis

Identifiers

PMID40297742
PMCPMC12037172

What OpenQuestion holds

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Registered trials

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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.