Evidence map›Paper›PMID 39221271›Full record

ArticlePeerJ2024

Comparisons of genome assembly tools for characterization of

Kanwara Trisakul, Yothin Hinwan, Jukgarin Eisiri, Kanin Salao, Angkana Chaiprasert, Phalin Kamolwat, Sissades Tongsima, Susana Campino, Jody Phelan, Taane G Clark and 1 more

Abstract readComparative Study
PubMed Full text at PMC Publisher
In one paragraph

Article in PeerJ, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing 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

2 citing papers in PubMed.

  1. Review
  2. 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

11 authors.

Kanwara TrisakulDepartment of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand.
Yothin HinwanDepartment of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand.
Jukgarin EisiriResearch and Diagnostic Center for Emerging Infectious Diseases (RCEID), Khon Kaen University, Khon Kaen, Thailand.
Kanin SalaoDepartment of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand.
Angkana ChaiprasertOffice for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.
Phalin KamolwatDivision of Tuberculosis, Department of Disease Control, Ministry of Public Health, Bangkok, Thailand.
Sissades TongsimaNational Biobank of Thailand, National Center for Genetics Engineering and Biotechnology, Pathum Thani, Thailand.ORCID 0000-0002-1491-1839
Susana CampinoFaculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, University of London, London, United Kingdom.
Jody PhelanFaculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, University of London, London, United Kingdom.
Taane G ClarkFaculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, University of London, London, United Kingdom.
Kiatichai FaksriDepartment of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Background: Next-generation sequencing of Methods: We compared the performance of genome assembly tools (Unicycler, RagOut, and RagTag) on sequence data from nine drug resistant Results: Our investigation found that Unicycler-based assemblies had significantly higher genome completeness (~98.7%; Conclusions: Unicycler software performed the best in terms of achieving contiguous genomes, whereas RagOut improved the quality of Unicycler's genome assemblies by providing a longer genome size. Overall, our approach has demonstrated that short-read and long-read hybrid assembly can provide a more complete genome assembly than short-read assembly alone by detecting pan-genomes and more genes, including IS

Indexed as

Genome, BacterialHigh-Throughput Nucleotide SequencingMycobacterium tuberculosisHumansPolymorphism, Single NucleotideSequence Analysis, DNAGenome assemblyHybrid assemblyMycobacterium tuberculosisNext-generation sequencingPan-genome

Identifiers

PMID39221271
PMCPMC11366230

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.