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