FLEA

FLEA analyzes long-read viral amplicon sequencing data to reconstruct high-quality consensus sequences (HQCSs) and infer phylogenetic and selection dynamics of viral populations.

Key Features:

• End-to-End Analysis Pipeline: Processes FASTQ reads to generate high-quality consensus sequences (HQCSs) for downstream analysis.
• Codon-Aware Multiple Sequence Alignment: Constructs codon-aware multiple sequence alignments from HQCSs to preserve reading frames for evolutionary analyses.
• Phylogenetic Inference and Evolutionary Dynamics: Infers phylogenies and assesses selection pressures, including gene-wide metrics such as dN/dS, to characterize evolutionary changes over time.
• Robustness to High Substitution and Indel Rates: Handles high substitution rates and extensive indel variation typical of complex viral genes such as HIV env.
• Error Rate Reduction Evaluation: Includes simulation-based evaluation demonstrating reduced error rates for Pacific Biosciences long-read sequencing, improving representation of complex viral populations.

Scientific Applications:

• HIV env gene dynamics: Reconstructs full-length HIV envelope (env) sequences to study sequence variation, selection, and implications for vaccine-relevant antigenic evolution.
• Viral population dynamics and resistance: Enables analysis of complete viral genes for investigations of population dynamics, drug resistance development, and immune escape across diverse viral systems.

Methodology:

Processes raw sequencing FASTQ reads into high-quality consensus sequences (HQCSs), constructs codon-aware multiple sequence alignments from HQCSs, and performs phylogenetic inference and selection-pressure assessment; simulation-based evaluation quantifies long-read sequencing error rates (e.g., Pacific Biosciences).