text: user1684: 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.
  
  user1075: Ragout worked well for me. It is a reference-based scaffolder.
  ragout.py --outdir output/ input/ragout.rcp > message.txt 2> 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.
  
original_text: 1684: <p>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.</p>
  
  <pre><code>mpiexec -n 1 Ray -k 55 -s 2-CA-SVA-2_S2_L001_R1_001.fastq_q30_trim_LR_15.fasta  -o rayd55tr
  </code></pre>
  
  <p>This worked quite well as I got a <code>scaffolds.fasta</code> file with two scaffolds one with 5730 bp and another with 1548 bp. </p>
  
  <p>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 :<a href="https://i.stack.imgur.com/SVhyo.jpg" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/SVhyo.jpg" alt="Blast of the manually joined contigs"></a>. </p>
  
  <p>Is there any tool to join these two contigs together to have one complete linear genome? I have reference genome too if needed.</p>
   1075: <p><a href="http://fenderglass.github.io/Ragout/" rel="nofollow noreferrer">Ragout</a> worked well for me. It is a reference-based scaffolder.</p>
  
  <pre><code>ragout.py --outdir output/ input/ragout.rcp &gt; message.txt 2&gt; error.txt --threads 8 --overwrite
  </code></pre>
  
  <p>The ragout.rcp file contains a 'recipe' with the reference sequence and the contigs in FASTA format.:</p>
  
  <pre><code>.references = ensembl
  .target = assembly
  
  ensembl.fasta = ref.fa
  assembly.fasta = contigs.fa
  </code></pre>
  
  <p>In my case, it reduced the number of contigs 10-fold and increased the N50 10-fold. It added N's between the contigs.</p>
  