Skip to Main content Skip to Navigation
Journal articles

StrainFLAIR: strain-level profiling of metagenomic samples using variation graphs

Kévin da Silva 1, 2, * Nicolas Pons 2 Magali Berland 2 Florian Plaza Oñate 2 Mathieu Almeida 2 Pierre Peterlongo 1
* Corresponding author
1 GenScale - Scalable, Optimized and Parallel Algorithms for Genomics
Inria Rennes – Bretagne Atlantique , IRISA-D7 - GESTION DES DONNÉES ET DE LA CONNAISSANCE
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 Escherichia coli, results show that StrainFLAIR was able to distinguish and estimate the abundances of close strains, as well as to highlight the presence of a new strain close to a referenced one and to estimate its abundance. On a real dataset composed of a mix of several bacterial species and several strains for the same species, results show that in a more complex configuration StrainFLAIR correctly estimates the abundance of each strain. Hence, results demonstrated how graph representation of multiple close genomes can be used as a reference to characterize a sample at the strain level.
Document type :
Journal articles
Complete list of metadata

https://hal.inria.fr/hal-03141144
Contributor : Pierre Peterlongo Connect in order to contact the contributor
Submitted on : Monday, August 23, 2021 - 11:52:29 AM
Last modification on : Friday, January 21, 2022 - 3:23:46 AM
Long-term archiving on: : Wednesday, November 24, 2021 - 6:23:17 PM

File

peerj-11884.pdf
Publication funded by an institution

Licence


Distributed under a Creative Commons Attribution 4.0 International License

Identifiers

Citation

Kévin da Silva, Nicolas Pons, Magali Berland, Florian Plaza Oñate, Mathieu Almeida, et al.. StrainFLAIR: strain-level profiling of metagenomic samples using variation graphs. PeerJ, PeerJ, 2021, ⟨10.7717/peerj.11884⟩. ⟨hal-03141144⟩

Share

Metrics

Les métriques sont temporairement indisponibles