# Stop on error. Print commands.
set -uex

# Download the genome data
efetch -db nuccore -id MG772933 -format fasta > MG772933.fa
efetch -db nuccore -id NC_045512 -format fasta > NC_045512.fa
  
# Align genomes globally.
# Replace needle with strecher for higher performance.
needle -filter  MG772933.fa NC_045512.fa  > alignment.txt