ArticleBioinformatics (Oxford, England)2019
BHap: a novel approach for bacterial haplotype reconstruction.
Article in Bioinformatics (Oxford, England), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Sequencing-based analysis of microbiomes.Nature reviews. Genetics · 2024Review
- Floria: fast and accurate strain haplotyping in metagenomes.Bioinformatics (Oxford, England) · 2024Article
- cgMSI: pathogen detection within species from nanopore metagenomic sequencing data.BMC bioinformatics · 2023Article
- Pitfalls of genotyping microbial communities with rapidly growing genome collections.Cell systems · 2023Article
- Statistical and Computational Methods for Microbial Strain Analysis.Methods in molecular biology (Clifton, N.J.) · 2023Review
- Article
- A revisit to universal single-copy genes in bacterial genomes.Scientific reports · 2022Article
- Scalable Microbial Strain Inference in Metagenomic Data Using StrainFacts.Frontiers in bioinformatics · 2022Article
- Reconstruction of evolving gene variants and fitness from short sequencing reads.Nature chemical biology · 2021Article
- Multilocus sequence analysis reveals genetic diversity in Staphylococcus aureus isolate of goat with mastitis persistent after treatment with enrofloxacin.Scientific reports · 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
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Authors and funding
4 authors.
Funding
Abstract
motivationThe bacterial haplotype reconstruction is critical for selecting proper treatments for diseases caused by unknown haplotypes. Existing methods and tools do not work well on this task, because they are usually developed for viral instead of bacterial populations.
resultsIn this study, we developed BHap, a novel algorithm based on fuzzy flow networks, for reconstructing bacterial haplotypes from next generation sequencing data. Tested on simulated and experimental datasets, we showed that BHap was capable of reconstructing haplotypes of bacterial populations with an average F1 score of 0.87, an average precision of 0.87 and an average recall of 0.88. We also demonstrated that BHap had a low susceptibility to sequencing errors, was capable of reconstructing haplotypes with low coverage and could handle a wide range of mutation rates. Compared with existing approaches, BHap outperformed them in terms of higher F1 scores, better precision, better recall and more accurate estimation of the number of haplotypes. AVAILABILITY AND IMPLEMENTATION: The BHap tool is available at http://www.cs.ucf.edu/∼xiaoman/BHap/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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