Phandango: an interactive viewer for bacterial population genomics

Hadfield, James; Croucher, Nicholas J.; Goater, Richard; Abudahab, Khalil; Aanensen, David M.; Harris, Simon R.

doi:10.1093/bioinformatics/btx610

Cited by 494 publications

(411 citation statements)

References 8 publications

(8 reference statements)

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“…Links to examples of such analyses are provided in Table 2. We have also included options for outputting the results of PopPUNK in formats appropriate for the online visualisation software Phandango (Hadfield et al 2017) and GrapeTree, the browser-based viewer used in Enterobase (Zhou et al 2017) . The underlying network can also be investigated using Cytoscape (Shannon et al 2003) .…”

Section: Poppunk Rapidly Integrates New Genomic Data Into Clustersmentioning

confidence: 99%

“…We therefore use dendropy or RapidNJ to produce a midpoint rooted neighbour joining tree from the core distances (Simonsen et al 2011;Sukumaran and Holder 2010) , and t-SNE to perform clustering of accessory distances . To enable interactive visualisation of these outputs, PopPUNK can write files formatted for Microreact (Argimón et al 2016) , Phandango (Hadfield et al 2017) and GrapeTree (Zhou et al 2017) . Each of these can be automatically joined with other user-provided metadata for visualisation.…”

Section: Output and Visualisationmentioning

confidence: 99%

See 1 more Smart Citation

Fast and flexible bacterial genomic epidemiology with PopPUNK

Lees

Harris

Tonkin‐Hill

et al. 2018

Preprint

120

186

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The routine use of genomics for disease surveillance provides the opportunity for high-resolution bacterial epidemiology.However, current whole-genome clustering and multi-locus typing approaches do not fully exploit core and accessory genomic variation, and cannot both automatically identify, and subsequently expand, clusters of significantly-similar isolates in large datasets and across species.Here we describe PopPUNK (Population Partitioning Using Nucleotide K-mers; https://poppunk.readthedocs.io/en/latest/ ), software implementing scalable and expandable annotation-and alignment-free methods for population analysis and clustering.Variable-length k -mer comparisons are used to distinguish isolates' divergence in shared sequence and gene content, which we demonstrate to be accurate over multiple orders of magnitude using both simulated data and real datasets from ten taxonomically-widespread species. Connections between closely-related isolates of the same strain are robustly identified, despite variation in the discontinuous pairwise distance distributions that reflects species' diverse evolutionary patterns. PopPUNK can process 10 3 -10 4 genomes as single batch, with minimal memory use and runtimes up to 200-fold faster than existing methods. Clusters of strains remain consistent as new batches of genomes are added, which is achieved without needing to re-analyse all genomes de novo.This facilitates real-time surveillance with stable cluster naming and allows for outbreak detection using hundreds of genomes in minutes. Interactive visualisation and online publication is streamlined through automatic output of results to multiple platforms.PopPUNK has been designed as a flexible platform that addresses important issues with currently used whole-genome clustering and typing methods, and has potential uses across bacterial genetics and public health research.

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Section: Poppunk Rapidly Integrates New Genomic Data Into Clustersmentioning

confidence: 99%

Section: Output and Visualisationmentioning

confidence: 99%

Fast and flexible bacterial genomic epidemiology with PopPUNK

Lees

Harris

Tonkin‐Hill

et al. 2018

Preprint

120

186

View full text Add to dashboard Cite

show abstract

“…A number of supplementary tools are provided to extract, align and subset sequences, and to compare and visualize outputs. In order to facilitate integration with existing pipeline, scripts have been provided to convert the outputs of PIRATE into common formats which allows for them to be used as inputs to software used for downstream analysis, such as the PanX user-interface, SCOARY, Microreact or Phandango [6,[15][16][17]. A full description of the methodology and comparative benchmarks has been provided in the supplementary information (Supplementary Information).…”

Section: Post-processingmentioning

confidence: 99%

PIRATE: A fast and scalable pangenomics toolbox for clustering diverged orthologues in bacteria

Bayliss

Thorpe

Coyle

et al. 2019

Preprint

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Cataloguing the distribution of genes within natural bacterial populations is essential for understanding evolutionary processes and the genetic basis of adaptation. Here we present a pangenomics toolbox, PIRATE (Pangenome Iterative Refinement And Threshold Evaluation), which identifies and classifies orthologous gene families in bacterial pangenomes over a wide range of sequence similarity thresholds. PIRATE builds upon recent scalable software developments to allow for the rapid interrogation of thousands of isolates. PIRATE clusters genes (or other annotated features) over a wide range of amino-acid or nucleotide identity thresholds and uses the clustering information to rapidly classify paralogous gene families into either putative fission/fusion events or gene duplications. Furthermore, PIRATE orders the pangenome using a directed graph, provides a measure of allelic variation and estimates sequence divergence for each gene family. We demonstrate that PIRATE scales linearly with both number of samples and computation resources, allowing for analysis of large genomic datasets, and compares favorably to other popular tools. PIRATE provides a robust framework for analysing bacterial pangenomes, from largely clonal to panmictic species.Availability: PIRATE is implemented in Perl and is freely available under an GNU GPL 3 open source license from https://github.com/SionBayliss/PIRATE. Contact: s.bayliss@bath.ac.uk

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“…This had the further advantage that it significantly reduced the number of sequence elements to be processed after association. Using selected unitigs allowed for a much smoother use of the interactive plotting software phandango (64) , which is one of the fastest ways to interpret bacterial GWAS results.…”

Section: Discussionmentioning

confidence: 99%

Improved inference and prediction of bacterial genotype-phenotype associations using pangenome-spanning regressions

Lees

Mai

Wheeler

et al. 2019

Preprint

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Discovery of influential genetic variants and prediction of phenotypes such as antibiotic resistance are becoming routine tasks in bacterial genomics. Genome-wide association study (GWAS) methods can be applied to study bacterial populations, with a particular emphasis on alignment-free approaches, which are necessitated by the more plastic nature of bacterial genomes. Here we advance bacterial GWAS by introducing a computationally scalable joint modeling framework, where genetic variants covering the entire pangenome are compactly represented by unitigs, and the model fitting is achieved using elastic net penalization. In contrast to current leading GWAS approaches, which test each genotype-phenotype association separately for each variant, our joint modelling approach is shown to lead to increased statistical power while maintaining control of the false positive rate. Our inference procedure also delivers an estimate of the narrow-sense heritability, which is gaining considerable interest in studies of bacteria. Using an extensive set of state-of-the-art bacterial population genomic datasets we demonstrate that our approach performs accurate phenotype prediction, comparable to popular machine learning methods, while retaining both interpretability and computational efficiency. We expect that these advances will pave the way for the next generation of high-powered association and prediction studies for an increasing number of bacterial species.

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Phandango: an interactive viewer for bacterial population genomics

Cited by 494 publications

References 8 publications

Fast and flexible bacterial genomic epidemiology with PopPUNK

Fast and flexible bacterial genomic epidemiology with PopPUNK

PIRATE: A fast and scalable pangenomics toolbox for clustering diverged orthologues in bacteria

Improved inference and prediction of bacterial genotype-phenotype associations using pangenome-spanning regressions

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