ArticlePeerJ2021
StrainFLAIR: strain-level profiling of metagenomic samples using variation graphs.
Article in PeerJ, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
What it found
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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.
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.
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Who cites it
6 citing papers in PubMed, 7 citations in OpenAlex.
- Sarand: exploring antimicrobial resistance gene neighbourhoods in complex metagenomic assembly graphs.NAR genomics and bioinformatics · 2026Article
- Resistance variation and bacterial interactions shape adaptation of a genetically diverse pathogen population to antibiotic therapy.The ISME journal · 2026Article
- Article
- Birthmode and environment-dependent microbiota transmission dynamics are complemented by breastfeeding during the first year.Cell host & microbe · 2024Article
- Community-scale models of microbiomes: Articulating metabolic modelling and metagenome sequencing.Microbial biotechnology · 2024Review
- Metagenomic Strain-Typing Combined with Isolate Sequencing Provides Increased Resolution of the Genetic Diversity ofMicroorganisms · 2023Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Current studies are shifting from the use of single linear references to representation of multiple genomes organised in pangenome graphs or variation graphs. Meanwhile, in metagenomic samples, resolving strain-level abundances is a major step in microbiome studies, as associations between strain variants and phenotype are of great interest for diagnostic and therapeutic purposes. We developed StrainFLAIR with the aim of showing the feasibility of using variation graphs for indexing highly similar genomic sequences up to the strain level, and for characterizing a set of unknown sequenced genomes by querying this graph. On simulated data composed of mixtures of strains from the same bacterial species
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Registered trials
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.