gistfile1.txt

#!/bin/bash

ec_ref="./E.coli.K12strainMG1655.fa"
dc_plas_ref="ecoli_plasmid.fa"

rm -f *.brg
rm -f *.bif

for space in 0 1
do
  for ref in $ec_ref $dc_plas_ref
  do
    bfast fasta2brg -A$space -f $ref

    bfast index -n8 -A$space -f $ref -m 111111111111111111 -w 12 -i 1 
    bfast index -n8 -A$space -f $ref -m 1111111110111111111 -w 12 -i 2 
    bfast index -n8 -A$space -f $ref -m 111111011111101011111 -w 12 -i 3 
    bfast index -n8 -A$space -f $ref -m 111111011001100111011111 -w 12 -i 4 
    bfast index -n8 -A$space -f $ref -m 1111011101011111101111 -w 12 -i 5
  done
done