StrainFLAIR: strain-level profiling of metagenomic samples using variation graphs
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 va...
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doaj-372d7ee034e448f196c6893f119d07f32021-08-25T15:05:05ZengPeerJ Inc.PeerJ2167-83592021-08-019e1188410.7717/peerj.11884StrainFLAIR: strain-level profiling of metagenomic samples using variation graphsKévin Da Silva0Nicolas Pons1Magali Berland2Florian Plaza Oñate3Mathieu Almeida4Pierre Peterlongo5Université Paris-Saclay, INRAE, MGP, Jouy-en-Josas, FranceUniversité Paris-Saclay, INRAE, MGP, Jouy-en-Josas, FranceUniversité Paris-Saclay, INRAE, MGP, Jouy-en-Josas, FranceUniversité Paris-Saclay, INRAE, MGP, Jouy-en-Josas, FranceUniversité Paris-Saclay, INRAE, MGP, Jouy-en-Josas, FranceUniv Rennes, Inria, CNRS, IRISA—UMR 6074, Rennes, FranceCurrent 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.https://peerj.com/articles/11884.pdfMetagenomicsVariation graphsStrain-level abundancesRead mapping |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Kévin Da Silva Nicolas Pons Magali Berland Florian Plaza Oñate Mathieu Almeida Pierre Peterlongo |
spellingShingle |
Kévin Da Silva Nicolas Pons Magali Berland Florian Plaza Oñate Mathieu Almeida Pierre Peterlongo StrainFLAIR: strain-level profiling of metagenomic samples using variation graphs PeerJ Metagenomics Variation graphs Strain-level abundances Read mapping |
author_facet |
Kévin Da Silva Nicolas Pons Magali Berland Florian Plaza Oñate Mathieu Almeida Pierre Peterlongo |
author_sort |
Kévin Da Silva |
title |
StrainFLAIR: strain-level profiling of metagenomic samples using variation graphs |
title_short |
StrainFLAIR: strain-level profiling of metagenomic samples using variation graphs |
title_full |
StrainFLAIR: strain-level profiling of metagenomic samples using variation graphs |
title_fullStr |
StrainFLAIR: strain-level profiling of metagenomic samples using variation graphs |
title_full_unstemmed |
StrainFLAIR: strain-level profiling of metagenomic samples using variation graphs |
title_sort |
strainflair: strain-level profiling of metagenomic samples using variation graphs |
publisher |
PeerJ Inc. |
series |
PeerJ |
issn |
2167-8359 |
publishDate |
2021-08-01 |
description |
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. |
topic |
Metagenomics Variation graphs Strain-level abundances Read mapping |
url |
https://peerj.com/articles/11884.pdf |
work_keys_str_mv |
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1721196401132568576 |