Viral Quasispecies Comparison from Long-Read Sequencing Data
Comparing viral quasispecies diversity metrics at amino acid level
Filtering highly dissimilar reads/sequences out of the alignment
Removing gap-rich positions and/or reads/sequences
longreadvqs: Viral Quasispecies Comparison from Long-Read Sequencing D...
Comparing operational taxonomic unit (OTU) by k-means clustering betwe...
Optimizing cut-off percentage for noise minimization
Pipe operator
Plotting single nucleotide variant (SNV) frequency in read alignment a...
Sequencing error and noise minimization, read down-sampling, and data ...
Comparing viral quasispecies profile and operational taxonomic unit (O...
Sequencing error and noise minimization with customized % cut-off at p...
Exporting viral quasispecies profile comparison results
Computing viral quasispecies diversity metrics of noise-minimized repe...
Computing viral quasispecies diversity metrics of noise-minimized down...
Performs variety of viral quasispecies diversity analyses [see Pamornchainavakul et al. (2024) <doi:10.21203/rs.3.rs-4637890/v1>] based on long-read sequence alignment. Main functions include 1) sequencing error and other noise minimization and read sampling, 2) Single nucleotide variant (SNV) profiles comparison, and 3) viral quasispecies profiles comparison and visualization.