ArticleMolecular biology and evolution2021
HAPHPIPE: Haplotype Reconstruction and Phylodynamics for Deep Sequencing of Intrahost Viral Populations.
Article in Molecular biology and evolution, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed, 17 citations in OpenAlex.
- An evaluation of computational methods for reconstruction of human viral DNA genomes.GigaScience · 2026Article
- V-pipe 3.0: a sustainable pipeline for within-sample viral genetic diversity estimation.GigaScience · 2024Article
- Pairwise comparative analysis of six haplotype assembly methods based on users' experience.BMC genomic data · 2023Article
- Applying the digital data and the bioinformatics tools in SARS-CoV-2 research.Computational and structural biotechnology journal · 2023Review
- Establishment and application of a method of tagged-amplicon deep sequencing for low-abundance drug resistance in HIV-1.Frontiers in microbiology · 2022Article
- Incorporating Within-Host Diversity in Phylogenetic Analyses for Detecting Clusters of New HIV Diagnoses.Frontiers in microbiology · 2021Article
- Validation of Variant Assembly Using HAPHPIPE with Next-Generation Sequence Data from Viruses.Viruses · 2020Article
- A cross-sectional study to characterize local HIV-1 dynamics in Washington, DC using next-generation sequencing.Scientific reports · 2020Article
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Authors and funding
6 authors at 1 institution in 2 countries.
Funding
Abstract
Deep sequencing of viral populations using next-generation sequencing (NGS) offers opportunities to understand and investigate evolution, transmission dynamics, and population genetics. Currently, the standard practice for processing NGS data to study viral populations is to summarize all the observed sequences from a sample as a single consensus sequence, thus discarding valuable information about the intrahost viral molecular epidemiology. Furthermore, existing analytical pipelines may only analyze genomic regions involved in drug resistance, thus are not suited for full viral genome analysis. Here, we present HAPHPIPE, a HAplotype and PHylodynamics PIPEline for genome-wide assembly of viral consensus sequences and haplotypes. The HAPHPIPE protocol includes modules for quality trimming, error correction, de novo assembly, alignment, and haplotype reconstruction. The resulting consensus sequences, haplotypes, and alignments can be further analyzed using a variety of phylogenetic and population genetic software. HAPHPIPE is designed to provide users with a single pipeline to rapidly analyze sequences from viral populations generated from NGS platforms and provide quality output properly formatted for downstream evolutionary analyses.
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Registered trials
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