Table 1 Summary of commands available in latest development version of rKOMICS
Command | Description |
|---|---|
Preprocess | Filters a FASTA file based on minicircle sequence length (specified by a minimum and maximum numeric value) and circularization success (Boolean argument) |
msc.length | Calculates and visualizes the length of minicircle sequences |
read.uc | Reads and stores USEARCH cluster format (UC) files |
msc.uc | Processes clustering results by estimating the number of MSCs and alignment insertions/deletions per minimum percent identity |
msc.matrix | Stores clustering results in a matrix where MSCs (rows) are classified as present (1) or absent (0) in each sample (columns) |
msc.heatmap | Creates a heatmap that summarizes the presence/absence of MSCs per sample and per group |
msc.richness | Summarizes and visualizes the number of MSCs per sample |
msc.similarity | Estimates the number and proportion of shared and unique MSCs between groups of samples |
msc.subset | Extracts specific MSCs for a given group of samples |
msc.pca | Principal Component Analysis to summarize MSC variation for all or a given set of samples |
msc.seqs | Retrieves the DNA sequence of a MSC together with all its hit sequences |
msc.quality | Checks the quality of the assembly |
msc.depth | Calculates the read depth and copy number of the assembled minicircles |