downloadNCBIGenomes: Function downloads genome fasta files from the NCBI FTP...

In kmeRtone: Multi-Purpose and Flexible k-Meric Enrichment Analysis Software

Function downloads genome fasta files from the NCBI FTP database. Users can provide either organism names or an assembly summary data table.

Description

Supports options for splitting multi-header fasta files and overwriting existing files.

Usage

downloadNCBIGenomes(
  asm,
  species,
  db,
  output.dir = "./",
  split.fasta = FALSE,
  overwrite = FALSE
)

Arguments

asm	NCBI assembly summary data.table
species	Species names.
db	Database record to use: refseq or genbank
output.dir	Output directory path. Default is current directory.
split.fasta	NCBI fasta files are multi-header. Split them? Default is FALSE.
overwrite	Overwrite any existed genome file? Default is FALSE to skip the download.

Value

Genome fasta file(s) named according to the FTP database convention.

kmeRtone documentation built on Sept. 11, 2024, 9:12 p.m.