D3GB (version 1.1)

getAssemblyFromFasta: Create an assembly from a FASTA file for its use as parameter of

Description

getAssemblyFromFasta create assemblies from a FASTA file for their use as parameter of genomebrowser or genomemap.

Usage

getAssemblyFromFasta(fasta)

Arguments

fasta

a "character" string representing the input Fasta file to be added in the genome browser.

Value

a data frame in BED format ready to use as an assembly in genomebrowser or genomemap.

See Also

The ‘D3GB’ Website: http://d3gb.usal.es genomebrowser, genomemap.

Examples

# Download fasta file
fasta <- tempfile()
download.file(paste0("ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/297/395/",
"GCF_000297395.2_ASM29739v2/GCF_000297395.2_ASM29739v2_genomic.fna.gz"),fasta)

# Assembly generation
getAssemblyFromFasta(fasta)