QSutils

QSutils provides utility functions for viral quasispecies analysis with NGS data, with most functions equally applicable to metagenomic studies.

Key Features:

• Data Manipulation and Exploration: Functions convert reads to haplotypes and frequencies, repair reads, intersect strand haplotypes, and visualize haplotype alignments.
• Diversity Indices: Functions compute diversity and entropy using incidence, abundance, and functional indices.
• Data Simulation: Functions generate random viral quasispecies data.

Scientific Applications:

• Viral Quasispecies Analysis: Analysis of viral quasispecies using NGS data.
• Metagenomic Studies: Application of utility functions to metagenomic data analysis.

Methodology:

The package implements three categories of methods: data manipulation and exploration for converting reads to haplotypes and frequencies, repairing reads, intersecting strand haplotypes, and visualizing haplotype alignments; diversity indices for computing diversity and entropy with incidence, abundance, and functional indices; and data simulation for generating random viral quasispecies data.