<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>

CC BY-SA 4.0
2018-11-26T07:26:32.977Z
2018-11-26T07:26:32.977Z
aechchiki
<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>

CC BY-SA 4.0
2018-11-23T10:32:53.290Z
2018-11-23T10:32:53.290Z
aechchiki
<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>

CC BY-SA 4.0
2018-11-22T16:15:36.310Z
http://dgenies.toulouse.inra.fr/
user172818
<phylogenetics><genome><software-recommendation><visualization>
full visualisation of draft genomes alignment
# 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 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.

**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 [@user172818](https://bioinformatics.stackexchange.com/users/37/user172818).


---

### 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)


---

