Reconstruction of Microbial Haplotypes by Integration of Statistical and Physical Linkage in Scaffolding

Chen Cao, Jingni He, Lauren Mak, Deshan Perera, Devin Kwok, Jia Wang, Minghao Li, Tobias Mourier, Stefan Gavriliuc, Matthew Greenberg, A. Sorana Morrissy, Laura K. Sycuro, Guang Yang, Daniel C. Jeffares, Quan Long

Research output: Contribution to journalArticlepeer-review


DNA sequencing technologies provide unprecedented opportunities to analyze within-host evolution of microorganism populations. Often, within-host populations are analyzed via pooled sequencing of the population, which contains multiple individuals or "haplotypes." However, current next-generation sequencing instruments, in conjunction with single-molecule barcoded linked-reads, cannot distinguish long haplotypes directly. Computational reconstruction of haplotypes from pooled sequencing has been attempted in virology, bacterial genomics, metagenomics, and human genetics, using algorithms based on either cross-host genetic sharing or within-host genomic reads. Here, we describe PoolHapX, a flexible computational approach that integrates information from both genetic sharing and genomic sequencing. We demonstrated that PoolHapX outperforms state-of-the-art tools tailored to specific organismal systems, and is robust to within-host evolution. Importantly, together with barcoded linked-reads, PoolHapX can infer whole-chromosome-scale haplotypes from 50 pools each containing 12 different haplotypes. By analyzing real data, we uncovered dynamic variations in the evolutionary processes of within-patient HIV populations previously unobserved in single position-based analysis.

Original languageEnglish
Pages (from-to)2660-2672
Number of pages13
JournalMolecular Biology and Evolution
Issue number6
Early online date6 Feb 2021
Publication statusPublished - 19 May 2021

Bibliographical note

Publisher Copyright:
© The Author(s) 2021. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.


  • haplotype reconstruction
  • linkage disequilibrium
  • regularization
  • within-host evolution

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