lola="/data4/Rifle/Moleculo/2.Moleculo-assembly/assembler/assemble.pl"
overlap="/home/itaish/software/QC/cpp/overlap/overlap"
moleculo_reads_file="RBG-1.reads.fna"

mkdir db
cd db
ln -s ../$moleculo_reads_file
formatdb -p F -o T -i $moleculo_reads_file
cd ..
echo "Running blast..."
blastall -p blastn -F F -m 8 -r 1 -q -5 -o RBG-1.reads.self.m8 -d db/$moleculo_reads_file -a 3 -i $moleculo_reads_file
echo "Running overlap..."
$overlap $moleculo_reads_file RBG-1.reads.self.m8 > RBG-1.reads.overlap.txt
echo "Running lola..."
$lola -p 99 $moleculo_reads_file RBG-1.reads.overlap.txt RBG-1.moleculo 2> RBG-1.moleculo.log
echo "Running done"
