Answers.Body: <p>Also, <a href="https://github.com/marbl/MashMap" rel="nofollow noreferrer">Mashmap</a> has an embedded <a href="https://github.com/marbl/MashMap#visualize" rel="nofollow noreferrer">visualisation tool</a> generating dot-plots to visualize mappings, ideal for:</p>
  
  <ul>
  <li>highly similar species or to compare different assemblies of the same species. </li>
  <li>mapping genome assembly or long reads (PacBio/ONT) to reference genome</li>
  </ul>
  
  <p>An example from their website: </p>
  
  <p><a href="https://i.sstatic.net/uIvbw.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/uIvbw.png" alt="enter image description here"></a></p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-11-26T07:26:32.977Z
Answers.LastActivityDate: 2018-11-26T07:26:32.977Z
Answers.UserDisplayName: aechchiki
Answers.Body: <p>Found a solution, using <a href="http://dgenies.toulouse.inra.fr/" rel="noreferrer">D-Genies</a>, worked great. </p>
  
  <p>Some examples from their website:</p>
  
  <p><a href="https://i.sstatic.net/Hhnul.png" rel="noreferrer"><img src="https://i.sstatic.net/Hhnul.png" alt="enter image description here"></a></p>
  
  <p>Thanks to <a href="https://bioinformatics.stackexchange.com/users/37/user172818">@user172818</a>.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-11-23T10:32:53.290Z
Answers.LastActivityDate: 2018-11-23T10:32:53.290Z
Answers.UserDisplayName: aechchiki
Body: <p>I have two draft genomes (aprox. 500Mb each), one with ~10'000 scaffolds (<code>genome1.fasta</code>) and one with ~1'000 contigs (<code>genome2.fasta</code>). I would like to visualize their pairwise alignment, which <a href="https://bioinformatics.stackexchange.com/questions/4139/visualisation-of-genome-alignment">a while ago</a> I found it could easily be done by <a href="http://mummer.sourceforge.net/manual/#mummerplot" rel="nofollow noreferrer">mummerplot</a> in <a href="http://mummer.sourceforge.net/" rel="nofollow noreferrer">MUMmer</a>.</p>
  
  <p>In mummer, <a href="http://mummer.sourceforge.net/manual/#aligningdraft" rel="nofollow noreferrer">pairwise draft genomes alignment</a> is supported:</p>
  
  <blockquote>
    <p>Many times it is necessary to align two genomes that have not yet been completed, or two genomes with multiple chromosomes. This can make things a little more complicated, since a separate alignment would have to be generated for each possible pairing of the sequences. However, both NUCmer and PROmer automate this process and accept multi-FastA inputs, thus simplifying the process of aligning two sets of contigs, scaffolds or chromosomes. </p>
  </blockquote>
  
  <p>It is still ok if I do it aligning small portions (e.g. contig vs scaffold), as I could get <a href="https://bioinformatics.stackexchange.com/a/4155/294">here</a>. However, if I do it all-vs-all, I end up with a "confetti"-plot (self-coined term) instead of a dot-plot : </p>
  
  <p><a href="https://i.sstatic.net/ggmtC.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/ggmtC.png" alt="enter image description here"></a></p>
  
  <p>I am not sure how to interpret this, and what I would like to see is more of a straight line as the one. Probably it's just a matter of filtering, so I'd like to ask for advice.</p>
  
  <p>I used <a href="http://mummer.sourceforge.net/manual/#nucmer" rel="nofollow noreferrer">nucmer</a> through <a href="http://mummer.sourceforge.net/manual/#filter" rel="nofollow noreferrer">delta-filter</a> as follows:</p>
  
  <pre><code># mummer version //4.0.0beta1 
  
  # nucmer
  nucmer --prefix=ref_qry genome1.fasta genome2.fasta
  
  # ref_qry.delta generated from previous step
  delta-filter -r -q ref_qry.delta &gt; ref_qry.filter
  
  # plot
  mummerplot ref_qry.filter -R genome1.fasta -Q genome2.fasta --filter --layout
  </code></pre>
  
  <p>Reasons for options <code>-r -q</code> in <code>delta-filter</code> step : </p>
  
  <blockquote>
    <p>To determine a one-to-one mapping of each reference and query, combine the options and use delta-filter -r -q.</p>
  </blockquote>
  
  <p>I'll also accept other methods for visualisation (doesn't need to be withh MUMmer). Any input is greatly appreciated!</p>
  
  <hr>
  
  <p><em>EDIT</em></p>
  
  <p>I found some solutions which I reported as answers. I will accept anyone giving answer on how to tune MUMmer parameters to achieve the goal I describe in the original question. </p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-11-22T16:15:36.310Z
Comments.Text: http://dgenies.toulouse.inra.fr/
Comments.UserDisplayName: user172818
Tags: <phylogenetics><genome><software-recommendation><visualization>
Title: full visualisation of draft genomes alignment
ThreadText: # full visualisation of draft genomes alignment
  
  (Asked by: username_0 on 2018-11-22)
  
  I have two draft genomes (aprox. 500Mb each), one with ~10'000 scaffolds (`genome1.fasta`) and one with ~1'000 contigs (`genome2.fasta`). I would like to visualize their pairwise alignment, which [a while ago](https://bioinformatics.stackexchange.com/questions/4139/visualisation-of-genome-alignment) I found it could easily be done by [mummerplot](http://mummer.sourceforge.net/manual/#mummerplot) in [MUMmer](http://mummer.sourceforge.net/).
  
  In mummer, [pairwise draft genomes alignment](http://mummer.sourceforge.net/manual/#aligningdraft) is supported:
  
  > Many times it is necessary to align two genomes that have not yet been completed, or two genomes with multiple chromosomes. This can make things a little more complicated, since a separate alignment would have to be generated for each possible pairing of the sequences. However, both NUCmer and PROmer automate this process and accept multi-FastA inputs, thus simplifying the process of aligning two sets of contigs, scaffolds or chromosomes.
  
  It is still ok if I do it aligning small portions (e.g. contig vs scaffold), as I could get [here](https://bioinformatics.stackexchange.com/a/4155/294). However, if I do it all-vs-all, I end up with a "confetti"-plot (self-coined term) instead of a dot-plot :
  
  [![enter image description here](https://i.sstatic.net/ggmtC.png)](https://i.sstatic.net/ggmtC.png)
  
  I am not sure how to interpret this, and what I would like to see is more of a straight line as the one. Probably it's just a matter of filtering, so I'd like to ask for advice.
  
  I used [nucmer](http://mummer.sourceforge.net/manual/#nucmer) through [delta-filter](http://mummer.sourceforge.net/manual/#filter) as follows:
  
  ```
  # mummer version //4.0.0beta1 
  
  # nucmer
  nucmer --prefix=ref_qry genome1.fasta genome2.fasta
  
  # ref_qry.delta generated from previous step
  delta-filter -r -q ref_qry.delta > ref_qry.filter
  
  # plot
  mummerplot ref_qry.filter -R genome1.fasta -Q genome2.fasta --filter --layout
  
  ```
  
  Reasons for options `-r -q` in `delta-filter` step :
  
  > To determine a one-to-one mapping of each reference and query, combine the options and use delta-filter -r -q.
  
  I'll also accept other methods for visualisation (doesn't need to be withh MUMmer). Any input is greatly appreciated!
  
  ---
  
  *EDIT*
  
  I found some solutions which I reported as answers. I will accept anyone giving answer on how to tune MUMmer parameters to achieve the goal I describe in the original question.
  
  **Tags:** phylogenetics, genome, software-recommendation, visualization
  
  > **Comments:**
  > **username_1**: http://dgenies.toulouse.inra.fr/  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_0 on 2018-11-23. Score: 6 | Accepted answer
  
  Found a solution, using [D-Genies](http://dgenies.toulouse.inra.fr/), worked great.
  
  Some examples from their website:
  
  [![enter image description here](https://i.sstatic.net/Hhnul.png)](https://i.sstatic.net/Hhnul.png)
  
  Thanks to [@username_1](https://bioinformatics.stackexchange.com/users/37/username_1).
  
  
  ---
  
  ### Answer by username_0 on 2018-11-26. Score: 1
  
  Also, [Mashmap](https://github.com/marbl/MashMap) has an embedded [visualisation tool](https://github.com/marbl/MashMap#visualize) generating dot-plots to visualize mappings, ideal for:
  
  * highly similar species or to compare different assemblies of the same species.
  * mapping genome assembly or long reads (PacBio/ONT) to reference genome
  
  An example from their website:
  
  [![enter image description here](https://i.sstatic.net/uIvbw.png)](https://i.sstatic.net/uIvbw.png)
  
  
  ---
  
  