I have downloaded the assembly fasta files for all chromosomes for an organism from NCBI. Now I want to map my unique data (WGS) to the genome. How to combine the chromosome-wise fasta files to give a fasta file for the whole genome? This needs to be done to run BWA, right?
`cat *.fa > genome.fa`

You'll need to index that with bwa or whatever aligner you plan to use then.