Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-11-27T11:55:38.940Z
Answers.Text: Please consider expanding your answer. How/when does it work well ? How will it help the OP in their case?
Answers.UserDisplayName: llrs
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-11-27T13:52:53.037Z
Answers.Text: I have added my code and what Ragout did for me. What does 'OP' mean?
Answers.UserDisplayName: Biomagician
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-11-27T15:42:30.400Z
Answers.Text: Great [edit]! OP comes from Original Poster to refer the one that asked the question. I hope this will be useful.
Answers.UserDisplayName: llrs
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-11-27T11:49:21.643Z
Answers.LastActivityDate: 2017-11-27T15:43:51.997Z
Answers.LastEditDate: 2017-11-27T15:43:51.997Z
Answers.UserDisplayName: Biomagician
Answers.Body: <p>In some cases you might consider reference-based scaffolding, as per <a href="https://bioinformatics.stackexchange.com/a/2944/196">charlesdarwin's answer</a>. I would argue that in most cases this will only provide limited information, as this will only really provide you with the order of the contigs <em>as it is in your reference</em>, as opposed to how it is in your sampled organism. In that sense it really only provides pseudo-scaffolding that makes your assembly look artificially good.</p>
  
  <p>In all cases you will have to check wether your raw data supports your scaffolding solution. </p>
  
  <p>Example: you will never be able to call structural variants across contig boundaries if you use reference based scaffolding. </p>
  
  <p>I would suggest you try different k-mer sized for your assembly algorithm, and look into dedicated scaffolding tools. Without knowing your type of sequencing data it is hard to suggest anything specific.</p>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-11-30T08:01:37.027Z
Answers.LastActivityDate: 2017-11-30T08:01:37.027Z
Answers.UserDisplayName: holmrenser
Body: <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.sstatic.net/SVhyo.jpg" rel="nofollow noreferrer"><img src="https://i.sstatic.net/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>
  
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-11-25T17:15:11.427Z
Comments.Text: What did you blast against? Your image just shows a few identical sequences, but we can't interpret any blast results without knowing what was blasted against what. Also, if you have a reference genome, why didn't you use that to assemble the contigs?
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-11-26T07:48:57.250Z
Comments.Text: Are there any good tools available for reference based contigs joining ?
Comments.UserDisplayName: LoveVirology
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-11-30T07:56:40.393Z
Comments.Text: It is quite important to know what kind of sequencing data you have used for people to provide accurate tips.
Comments.UserDisplayName: holmrenser
Tags: <ngs>
Title: Joining scaffolds to get full genome?
ThreadText: # Joining scaffolds to get full genome?
  
  (Asked by: username_0 on 2017-11-24)
  
  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 :[![Blast of the manually joined contigs](https://i.sstatic.net/SVhyo.jpg)](https://i.sstatic.net/SVhyo.jpg).
  
  Is there any tool to join these two contigs together to have one complete linear genome? I have reference genome too if needed.
  
  **Tags:** ngs
  
  > **Comments:**
  > **username_1**: What did you blast against? Your image just shows a few identical sequences, but we can't interpret any blast results without knowing what was blasted against what. Also, if you have a reference genome, why didn't you use that to assemble the contigs?  
  > **username_0**: Are there any good tools available for reference based contigs joining ?  
  > **username_2**: It is quite important to know what kind of sequencing data you have used for people to provide accurate tips.  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_3 on 2017-11-27. Score: 2
  
  [Ragout](http://fenderglass.github.io/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.
  
  > **Comments:**
  > **username_4**: Please consider expanding your answer. How/when does it work well ? How will it help the OP in their case?  
  > **username_3**: I have added my code and what Ragout did for me. What does 'OP' mean?  
  > **username_4**: Great [edit]! OP comes from Original Poster to refer the one that asked the question. I hope this will be useful.  
  
  ---
  
  ### Answer by username_2 on 2017-11-30. Score: 0
  
  In some cases you might consider reference-based scaffolding, as per [charlesdarwin's answer](https://bioinformatics.stackexchange.com/a/2944/196). I would argue that in most cases this will only provide limited information, as this will only really provide you with the order of the contigs *as it is in your reference*, as opposed to how it is in your sampled organism. In that sense it really only provides pseudo-scaffolding that makes your assembly look artificially good.
  
  In all cases you will have to check wether your raw data supports your scaffolding solution.
  
  Example: you will never be able to call structural variants across contig boundaries if you use reference based scaffolding.
  
  I would suggest you try different k-mer sized for your assembly algorithm, and look into dedicated scaffolding tools. Without knowing your type of sequencing data it is hard to suggest anything specific.
  
  
  ---
  
  