# Viral Quasispecies Comparison from Long-Read Sequencing Data

## Documentation for package ‘longreadvqs’ version 0.1.5

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

AAcompare | Comparing viral quasispecies diversity metrics at amino acid level
filtfast | Filtering highly dissimilar reads/sequences out of the alignment
gapremove | Removing gap-rich positions and/or reads/sequences
otucompare | Comparing operational taxonomic unit (OTU) by k-means clustering between samples
pctopt | Optimizing cut-off percentage for noise minimization
snvcompare | Plotting single nucleotide variant (SNV) frequency in read alignment across different samples
vqsassess | Sequencing error and noise minimization, read down-sampling, and data preparation for viral quasispecies comparison
vqscompare | Comparing viral quasispecies profile and operational taxonomic unit (OTU) classified by k-means clustering between samples
vqscustompct | Sequencing error and noise minimization with customized % cut-off at particular nucleotide region, read down-sampling, and data preparation for viral quasispecies comparison
vqsout | Exporting viral quasispecies profile comparison results
vqsresub | Computing viral quasispecies diversity metrics of noise-minimized repeatedly down-sampled read alignments
vqssub | Computing viral quasispecies diversity metrics of noise-minimized down-sampled read alignment