text: user294: 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 I found it could easily be done by mummerplot in MUMmer.
  In mummer, pairwise draft genomes alignment 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. However, if I do it all-vs-all, I end up with a "confetti"-plot (self-coined term) instead of a dot-plot : 
  
  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 through delta-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. 
  
  user294: Also, Mashmap has an embedded visualisation tool 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: 
  
  
  user294: Found a solution, using D-Genies, worked great. 
  Some examples from their website:
  
  Thanks to @user172818.
  
original_text: 294: <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.stack.imgur.com/ggmtC.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/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>
   294: <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.stack.imgur.com/uIvbw.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/uIvbw.png" alt="enter image description here"></a></p>
   294: <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.stack.imgur.com/Hhnul.png" rel="noreferrer"><img src="https://i.stack.imgur.com/Hhnul.png" alt="enter image description here"></a></p>
  
  <p>Thanks to <a href="https://bioinformatics.stackexchange.com/users/37/user172818">@user172818</a>.</p>
  