HAPHPIPE

HAPHPIPE reconstructs viral haplotypes and assembles consensus sequences from next-generation sequencing (NGS) data to quantify intra-host viral variation for evolutionary and phylogenetic analyses.

Key Features:

• NGS data processing: Operates on next-generation sequencing (NGS) viral datasets for downstream assembly and analysis.
• De novo assembly: Performs de novo assembly of viral NGS datasets.
• Reference-based assembly: Performs reference-based assembly of viral NGS datasets.
• Consensus sequence assembly: Constructs consensus sequences that capture sequence variation including low-abundance variants.
• Haplotype reconstruction and intra-host variation quantification: Reconstructs haplotypes to quantify intra-host viral diversity.
• Validation and comparison: Validated with simulated and empirical datasets from HIV, HCV, and SARS-CoV-2 and compared to HyDRA and Geneious, producing pol consensus sequences closer to the true consensus and gp120 consensus performance comparable to Geneious.
• Computational efficiency: Provides computational speed suitable for analysis of larger sequence datasets.

Scientific Applications:

• Intra-host diversity analysis: Quantifies intra-host viral diversity for HIV, HCV, SARS-CoV-2, and other viruses.
• Evolutionary and phylogenetic studies: Generates haplotypes and consensus sequences for phylogenetic and evolutionary inference.
• Clinical and vaccine research: Provides intra-host variation data that can inform treatment strategies and vaccine development.

Methodology:

Processes NGS data using de novo and reference-based assembly, performs haplotype reconstruction and consensus sequence construction, and was validated with simulated and empirical HIV, HCV, and SARS-CoV-2 datasets with comparative analyses against HyDRA and Geneious.