Viral Quasispecies Comparison from Long-Read Sequencing Data

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Documentation for package ‘longreadvqs’ version 0.1.3

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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