non_redundant_pangenomes: Non redundant pangenomes.

In irycisBioinfo/PATO: Pangenome Analysis Toolkit

Non redundant pangenomes.

Description

Remove redundant sequences from a file list of sequences (nucleotide or protein).

Usage

non_redundant_pangenomes(
  file_list,
  distance,
  type = "prot",
  n_cores,
  sketch = 1000,
  kmer = 21
)

Arguments

file_list	A data.frame with the path list of files or a gff_list object.
distance	Sequence distance (<1)
type	"nucl" or "prot"
n_cores	number of cores to use (default: total cores -1)
sketch	sketch size (mash option)
kmer	kmer size (mash option)

Details

This function has been designed to remove redundant sequences from a dataset. Unlike other non redundant functions, this function only accept a distance threshold and has been designed to remove very similar sequences (>99.9%)

irycisBioinfo/PATO documentation built on Oct. 19, 2023, 3:07 p.m.