Mar 31, 2020

De novo reconstruction of microbial haplotypes by integrating statistical and physical linkage

BioRxiv : the Preprint Server for Biology
Ruth E BakerQuan Long

Abstract

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 demonstrate that PoolHapX outperforms state-of-the-art tools in the above four fields, and is robust to within-host evolution. Importantly, together with barcoded linked-reads, PoolHapX can infer whole-chromosome-scale haplotypes from pools with 20 different haplotypes. By analyzing real data, we have uncovered dynamic variations in the evolutionary processes of HIV previously unobserved in single position-based analysis.

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