Indexes the FASTA file, and generates a ‘chrom.sizes’ file

Source: R/process_reads.R

Indexes the FASTA file, and generates a ‘chrom.sizes’ file with chromosome numbers and the size of each chromosome.

index_fa(fa_file, chromsize_file = "chrom.sizes", outdir = dirname(fa_file))

Arguments

fa_file

FASTA file of reference genome sequence.

chromsize_file

Path of the output ‘chrom.sizes’ file.

outdir

Output directory (default: saves to the directory of the FASTA file).

Examples

if (FALSE) {
index_fa('hg38.fa', chromsize_file='hg38.chrom.sizes')
}