Joining scaffolds to get full genome? I am using Ray to assemble a about 7.2 kb picornavirus genome. I am using k-mer of 55. Following is the exact code that I used.

mpiexec -n 1 Ray -k 55 -s 2-CA-SVA-2_S2_L001_R1_001.fastq_q30_trim_LR_15.fasta  -o rayd55tr


This worked quite well as I got a scaffolds.fasta file with two scaffolds one with 5730 bp and another with 1548 bp. 

Now, I am confused how I can join those scaffolds to get one linear genome. I joined them manually and blasted just to check and I got something like below :. 

Is there any tool to join these two contigs together to have one complete linear genome? I have reference genome too if needed.
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.