ArticleNucleic acids research2015
Frequency-based haplotype reconstruction from deep sequencing data of bacterial populations.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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32 citing papers in PubMed.
- Benchmarking of Reference-Based Tools for Strain-Level Resolution of Plant Microbiome.Molecular ecology resources · 2026Article
- Embracing Complexity: What Novel Sequencing Methods Are Teaching Us About Herpesvirus Genomic Diversity.Annual review of virology · 2024Review
- Floria: fast and accurate strain haplotyping in metagenomes.Bioinformatics (Oxford, England) · 2024Article
- ColiSeq: a multiplex amplicon assay that provides strain level resolution ofMicrobiology spectrum · 2024Article
- SNP-slice resolves mixed infections: simultaneously unveiling strain haplotypes and linking them to hosts.Bioinformatics (Oxford, England) · 2024Article
- Article
- Pitfalls of genotyping microbial communities with rapidly growing genome collections.Cell systems · 2023Article
- Article
- Combination of Whole Genome Sequencing and Metagenomics for Microbiological Diagnostics.International journal of molecular sciences · 2022Review
- A revisit to universal single-copy genes in bacterial genomes.Scientific reports · 2022Article
- Comparative 3D genome architecture in vertebrates.BMC biology · 2022Article
- Haplotype assignment of longitudinal viral deep sequencing data using covariation of variant frequencies.Virus evolution · 2022Article
- The evolution of bacterial genome assemblies - where do we need to go next?Microbiome research reports · 2022Article
- Reconstruction of evolving gene variants and fitness from short sequencing reads.Nature chemical biology · 2021Article
- Reconstruction of Microbial Haplotypes by Integration of Statistical and Physical Linkage in Scaffolding.Molecular biology and evolution · 2021Article
- mixtureS: a novel tool for bacterial strain genome reconstruction from reads.Bioinformatics (Oxford, England) · 2021Article
- Article
- Strain-Level Metagenomic Data Analysis of Enriched In Vitro and In Silico Spiked Food Samples: Paving the Way towards a Culture-Free Foodborne Outbreak Investigation Using STEC as a Case Study.International journal of molecular sciences · 2020Article
- Computational Methods for Strain-Level Microbial Detection in Colony and Metagenome Sequencing Data.Frontiers in microbiology · 2020Review
- BHap: a novel approach for bacterial haplotype reconstruction.Bioinformatics (Oxford, England) · 2019Article
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9 authors.
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Abstract
Clonal populations accumulate mutations over time, resulting in different haplotypes. Deep sequencing of such a population in principle provides information to reconstruct these haplotypes and the frequency at which the haplotypes occur. However, this reconstruction is technically not trivial, especially not in clonal systems with a relatively low mutation frequency. The low number of segregating sites in those systems adds ambiguity to the haplotype phasing and thus obviates the reconstruction of genome-wide haplotypes based on sequence overlap information.Therefore, we present EVORhA, a haplotype reconstruction method that complements phasing information in the non-empty read overlap with the frequency estimations of inferred local haplotypes. As was shown with simulated data, as soon as read lengths and/or mutation rates become restrictive for state-of-the-art methods, the use of this additional frequency information allows EVORhA to still reliably reconstruct genome-wide haplotypes. On real data, we show the applicability of the method in reconstructing the population composition of evolved bacterial populations and in decomposing mixed bacterial infections from clinical samples.
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