Script to merge contigs generated using different de novo assembly methods. It uses blastn to map contigs to a reference sequence.
git clone https://github.com/vbsreenu/ContigsMerger.git
cd ContigsMerger
chmod +x contigsMerger
contigsMerger reference.fa contigs.fa N
if you want to fill the gaps with reference sequence
contigsMerger reference.fa contigs.fa