Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-11-05T13:46:05.793Z
Answers.LastActivityDate: 2017-11-05T13:46:05.793Z
Answers.UserDisplayName: Bioathlete
Body: <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>
  
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-11-05T00:26:00.060Z
Comments.Text: Blat the contigs
Comments.UserDisplayName: SmallChess
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-11-05T00:28:17.517Z
Comments.Text: Would you mind elaborating ?
Comments.UserDisplayName: LoveVirology
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-11-05T23:13:01.307Z
Comments.Text: How to proceed depends entirely on  what you want the assembly for. Are you looking for variants? Is this the genome of a related species which has not been annotated and you want to find its genes? Are you looking for one gene in particular? For syntenic regions? We can't tell you how to proceed if you don't tell us what you need. Please [edit] your question and clarify.
Comments.UserDisplayName: terdon
Tags: <ngs>
Title: How to proceed after contigs.fa file obtained from VELVET assembly
ThreadText: # How to proceed after contigs.fa file obtained from VELVET assembly
  
  (Asked by: username_0 on 2017-11-04)
  
  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?
  
  **Tags:** ngs
  
  > **Comments:**
  > **username_1**: Blat the contigs  
  > **username_0**: Would you mind elaborating ?  
  > **username_2**: How to proceed depends entirely on  what you want the assembly for. Are you looking for variants? Is this the genome of a related species which has not been annotated and you want to find its genes? Are you looking for one gene in particular? For syntenic regions? We can't tell you how to proceed if you don't tell us what you need. Please [edit] your question and clarify.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_3 on 2017-11-05. Score: 3
  
  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?
  
  
  ---
  
  