Evidence map›Paper›PMID 37043380›Full record

ArticleMicrobial genomics2023

Comparing genomic variant identification protocols for

Xiao Li, José F Muñoz, Lalitha Gade, Silvia Argimon, Marie-Elisabeth Bougnoux, Jolene R Bowers, Nancy A Chow, Isabel Cuesta, Rhys A Farrer, Corinne Maufrais and 16 more

Open access · goldAbstract readComparative Study
PubMed Full text at PMC Publisher
In one paragraph

Article in Microbial genomics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.

0numbers the graph read from it
0cells of the map it votes in
7citing papers in PubMed
2.5field-weighted citation impact, top 11% of its field
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

7 citing papers in PubMed, 13 citations in OpenAlex.

  1. Review
  2. Article
  3. RapidmSphere · 2025
    Article
  4. Population structure, resistome, and virulome ofFrontiers in cellular and infection microbiology · 2025
    Article
  5. Review
  6. IdentifyingJournal of clinical microbiology · 2024
    Article
  7. 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

26 authors at 14 institutions in 7 countries.

Xiao LiBroad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
José F MuñozBroad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
Lalitha GadeMycotic Diseases Branch, Centers for Disease Control and Prevention, US Department of Health and Human Services, Atlanta, GA, 30329, USA.
Silvia ArgimonCentre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Oxford, UK.
Marie-Elisabeth BougnouxInstitut Pasteur, Université Paris Cité, INRAE, USC2019, Unité Biologie et Pathogénicité Fongiques, Paris, France.
Jolene R BowersTranslational Genomics Research Institute, Pathogen and Microbiome Division, Flagstaff, AZ 86005, USA.
Nancy A ChowMycotic Diseases Branch, Centers for Disease Control and Prevention, US Department of Health and Human Services, Atlanta, GA, 30329, USA.
Isabel CuestaMycology Reference Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III, Madrid, Spain.
Rhys A FarrerBroad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
Corinne MaufraisInstitut Pasteur, Université Paris Cité, INRAE, USC2019, Unité Biologie et Pathogénicité Fongiques, Paris, France.
Juan Monroy-NietoTranslational Genomics Research Institute, Pathogen and Microbiome Division, Flagstaff, AZ 86005, USA.
Dibyabhaba PradhanAll India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India.
Jessie UehlingBotany and Plant Pathology, Oregon State University, Corvallis, OR 97330, USA.
Duong VuWesterdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584CT, Utrecht, Netherlands.
Corin A YeatsCentre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Oxford, UK.
David M AanensenCentre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Oxford, UK.
Christophe d'EnfertInstitut Pasteur, Université Paris Cité, INRAE, USC2019, Unité Biologie et Pathogénicité Fongiques, Paris, France.
David M EngelthalerTranslational Genomics Research Institute, Pathogen and Microbiome Division, Flagstaff, AZ 86005, USA.
David W EyreNIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK.
Matthew C FisherMRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK.
Ferry HagenWesterdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584CT, Utrecht, Netherlands.
Wieland MeyerSydney Medical School, University of Sydney, Sydney, NSW 2050, Australia.
Gagandeep SinghAll India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India.
Ana Alastruey-IzquierdoMycology Reference Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III, Madrid, Spain.
Anastasia P LitvintsevaMycotic Diseases Branch, Centers for Disease Control and Prevention, US Department of Health and Human Services, Atlanta, GA, 30329, USA.
Christina A CuomoBroad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
Broad Institute · USUniversity of Oxford · GBCenters for Disease Control and Prevention · USTranslational Genomics Research Institute · USAll India Institute of Medical Sciences · INInstituto de Salud Carlos III · ESCentre National de la Recherche Scientifique · FRHôpital Necker-Enfants Malades · FRImperial College London · GBInstitut Pasteur · FROregon State University · USThe University of Sydney · AUUniversity Medical Center Utrecht · NLWesterdijk Fungal Biodiversity Institute · NL

Funding

Viral Genomics: evolution, spread, and host interactionsU19AI110818 · NIAID · BROAD INSTITUTE, INC. · PI SABETI, PARDIS CHRISTINE · 2014 to 2024
$66.5M
Medical Research Council MR/R015600/1Medical Research Council MR/V033417/1NIAID NIH HHS U19 AI110818
6 · The paper itself

Abstract

Genomic analyses are widely applied to epidemiological, population genetic and experimental studies of pathogenic fungi. A wide range of methods are employed to carry out these analyses, typically without including controls that gauge the accuracy of variant prediction. The importance of tracking outbreaks at a global scale has raised the urgency of establishing high-accuracy pipelines that generate consistent results between research groups. To evaluate currently employed methods for whole-genome variant detection and elaborate best practices for fungal pathogens, we compared how 14 independent variant calling pipelines performed across 35

Indexed as

Candida aurisCandidiasisDisease OutbreaksDrug Resistance, FungalGenome, FungalHumansPhylogenyPolymorphism, Single NucleotidebenchmarkingCandidafungal genomicsvariant calling pipelineswhole-genome sequencing

Identifiers

PMID37043380
PMCPMC10210944
OpenAlexW4365135538

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.