HAPHPIPE: Haplotype Reconstruction and Phylodynamics for Deep Sequencing of Intrahost Viral Populations
| Autor: | Matthew L. Bendall, Keylie M. Gibson, Keith A. Crandall, Uzma Rentia, Marcos Pérez-Losada, Margaret C. Steiner |
|---|---|
| Rok vydání: | 2020 |
| Předmět: |
Population
Sequence assembly Computational biology Genome Viral Biology AcademicSubjects/SCI01180 Genome molecular epidemiology Deep sequencing 03 medical and health sciences transmission cluster 0302 clinical medicine Genetics Consensus sequence Protocol education Molecular Biology Ecology Evolution Behavior and Systematics Phylogeny 030304 developmental biology 0303 health sciences education.field_of_study Phylogenetic tree Haplotype AcademicSubjects/SCI01130 High-Throughput Nucleotide Sequencing HIV bioinformatics phylodynamics Viral phylodynamics Haplotypes 030217 neurology & neurosurgery Software |
| Zdroj: | Molecular Biology and Evolution |
| ISSN: | 1537-1719 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
| Externí odkaz: |
|