text: user1684: I want to assemble a linear genome and I have a reference genome too.
  I ran the following commands for de novo velvet assembly: 
  velveth auto 31,45,2 -fastq -shortPaired1 -separate 2-CA-SVA-2_S2_L001_R1_001.fastq 2-CA-SVA-2_S2_L001_R2_001.fastq
  
  I chose auto_33 for further analysis
  velvetg auto_33 -exp_cov auto
  
  Now my output files inside auto_33 folder are:
  contigs.fa
  Graph2
  LastGraph
  Log
  PreGraph
  Roadmaps
  Sequences
  stats.txt
  
  But I have no clue how to move ahead. Can I do anything else with velvet or do I have to switch to another program?
  
  user964: The contigs.fa file is a FASTA formatted file of the final contigs generated by velvet.  I would start assessing the quality of the assembly that was generated. Here are some questions to get you started.  Really the next steps depend on how you plan to use the assembly.
  What is the distribution of contig lengths? Average and N50 contig length
  How does the assembly compare to the reference?
  
  How much of the reference does the assembly cover?
  
  When you align the original reads back to the contigs how well are they covered? 
  
  Do any of the read alignments not make sense? 
  Are there sections of the contigs that are not covered?
  
  
original_text: 1684: <p>I want to assemble a linear genome and I have a reference genome too.</p>
  
  <p>I ran the following commands for de novo velvet assembly: </p>
  
  <pre><code>velveth auto 31,45,2 -fastq -shortPaired1 -separate 2-CA-SVA-2_S2_L001_R1_001.fastq 2-CA-SVA-2_S2_L001_R2_001.fastq
  </code></pre>
  
  <p>I chose auto_33 for further analysis</p>
  
  <pre><code>velvetg auto_33 -exp_cov auto
  </code></pre>
  
  <p>Now my output files inside auto_33 folder are:</p>
  
  <pre><code>contigs.fa
  Graph2
  LastGraph
  Log
  PreGraph
  Roadmaps
  Sequences
  stats.txt
  </code></pre>
  
  <p>But I have no clue how to move ahead. Can I do anything else with velvet or do I have to switch to another program?</p>
   964: <p>The contigs.fa file is a FASTA formatted file of the final contigs generated by velvet.  I would start assessing the quality of the assembly that was generated. Here are some questions to get you started.  Really the next steps depend on how you plan to use the assembly.</p>
  
  <p>What is the distribution of contig lengths? Average and N50 contig length</p>
  
  <p>How does the assembly compare to the reference?</p>
  
  <ul>
  <li>How much of the reference does the assembly cover?</li>
  </ul>
  
  <p>When you align the original reads back to the contigs how well are they covered? </p>
  
  <ul>
  <li><p>Do any of the read alignments not make sense? </p></li>
  <li><p>Are there sections of the contigs that are not covered?</p></li>
  </ul>
  