Joining scaffolds to get full genome?
Ragout worked well for me. It is a reference-based scaffolder.

ragout.py --outdir output/ input/ragout.rcp &gt; message.txt 2&gt; error.txt --threads 8 --overwrite


The ragout.rcp file contains a 'recipe' with the reference sequence and the contigs in FASTA format.:

.references = ensembl
.target = assembly

ensembl.fasta = ref.fa
assembly.fasta = contigs.fa


In my case, it reduced the number of contigs 10-fold and increased the N50 10-fold. It added N's between the contigs.