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Assembly statistic visualisation

Home Page: http://genomehubs.org

License: MIT License

HTML 8.75% CSS 9.52% JavaScript 71.93% Perl 9.79%

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help running the program

Hi,
Thank you for writing this wonderful program. These figures look really nice.
However, as I have no knowledge of the java program and being a newbie in bioinformatics. I have not been able to run the program.

What I did was:

I downloaded the repository assembly-stats on my home folder
created the input file called output.json using asm2stats.pl script and placed it in the assembly-stats/json folder.
Configured web successfully following the link suggested in issue 10
I then tried to use this link below to run it in the safari browser.
http://localhost/~/assembly-stats/assembly-stats.html?path=/~/assembly-stats/json/&assembly=output&view=circle&altView=cumulative&altView=table

But it says The requested URL was not found on this server.
I also tried with the test JSON file the same way and it's the same error.

I am also confused with the scripts you provided in usage section for where to use.

Can you please help me with it?

Thank you,
Upendra

How to cite

Aloha!

Can you provide a citation that we can use to reference this program?

Thanks!
Sheina

I have issues...

Hi Rich,

made the plots for two assemblies with the previous version and they are great.

what do you think about replacing the colouring of the outer GC-band with a wiggle/dot-plot of GC and N's for each scaffold (using fixed windowsize or scaffold/contig mean)?

that way one could tell wether for example half of the biggest scaffold is made up of N's ... or if you have GC outlier in the biggest scaffolds.

cheers,

dom

Can't get a web resulted?

I'm following README file written this html file, but get an empty web page when opening it with google chrome.

<html>
<head>
    <title>assembly stats</title>
  </head>
  <body>
    <link rel="stylesheet" type="text/css" href="css/circle-plot.css">
    <link rel="stylesheet" type="text/css" href="css/square-plot.css">
    <link rel="stylesheet" type="text/css" href="css/table.css">
    <script src="https://ajax.googleapis.com/ajax/libs/jquery/1.12.2/jquery.min.js"></script>
    <script src="https://d3js.org/d3.v3.min.js" charset="utf-8"></script>
    <script src="http://labratrevenge.com/d3-tip/javascripts/d3.tip.v0.6.3.js"></script>
    <script type="text/javascript" src="js/circle-plot.js"></script>
    <script type="text/javascript" src="js/square-plot.js"></script>
    <script type="text/javascript" src="js/table.js"></script>
    <div id="assembly_stats">
    <script charset="utf-8" src="d3.js"></script>
    <script>
      d3.json("Danaus_plexippus_v3.assembly-stats.json", function(error, json) {
        if (error) return console.warn(error);
        asm = new Assembly (json);
        asm.drawPlot('assembly_stats');
      })
    </script>

  </body>
</html>

json produced by perl scripts not working?

i have the program working locally (tested it on the example jsons provided). However, it displays a blank white screen when i substitute these for my own jsons generated by either of the asm2stat scripts.

i noticed that the order of the keys in my jsons were different in my so wrote a script to reorder them based on those in the Danaus file. this seems to fix it but I was just a bit confused why this was happening and wanted to flag it should it be affecting anyone else.

live demo link broken

The link to the live demo is not working http://content.lepbase.org/pages/assemblies/assembly-stats.html?assembly=Danaus_plexippus_v3&altAssembly=Heliconius_melpomene_Hmel2&view=compare&altView=circle&altView=cumulative&altView=table

Using assembly-stats for MAGs

Hi @rjchallis - I came across your repo yesterday and I'm very eager to use assembly-stats because I have been wanting to visualize my assembly stats just like your tool does. I spent a lot of time looking at the circulize package in R, but it's a beast with which I don't wish to mess.

But before I use your scripts, I have a few questions, please. I work with metagenomic assembled genomes (MAGs) which are essentially a bunch of single genomes. I want to compare the assembly stats of about 10-20 MAGs per sample, so can I:

Compare more than two genomes/MAGs at the same time using your tool?
Use genome completion stats from CheckM instead of CEGMA?
Include coverage data in the circular plots for each genome/MAG?

I look forward to hearing from you. Thank you so much for your help!

Taruna

Illegal division by zero at ./asm2stats.minmaxgc.pl line 131

I got
Illegal division by zero at ./asm2stats.minmaxgc.pl line 131 when trying to run asm2stats.minmaxgc.pl on data of this two files:

https://i5k.nal.usda.gov/data/Arthropoda/nicves-(Nicrophorus_vespilloides)/Current%20Genome%20Assembly/1.Genome%20Assembly/GCF_001412225.1/Scaffolds/GCF_001412225.1_Nicves_v1.0_genomic_RefSeqIDs.fna.gz

https://i5k.nal.usda.gov/data/Arthropoda/tricas-(Tribolium_castaneum)/Current%20Genome%20Assembly/1.Genome%20Assembly/Tcas5.2-GCF_000002335.3/Scaffolds/GCF_000002335.3_Tcas5.2_genomic_RefSeqIDs.fna.gz

I just look into the file, I think the problem maybe due to the mixed lowercase and uppercase of the fasta file. Can you update the perl script for that ? Sorry, I want to help but doesn't so familiar with perl....

is there a way to download a static plot as a vector image (e.g. PDF or .svg?)

Hello Richard,
These are really great. Do you know of an easy way to download the d3 object as a static image? I've googled around and none of the solutions that I have found seem to work very well. If you have any advice, that would be great!

Thanks,

Paul Frandsen

How to proceed after generating JSON file?

Hello,

I know this is a basic question, but I was wondering how to proceed after using one of the perl scripts to generate a JSON file? How can I get the webpage? Is "assembly-stats.html" used as a template where you insert the example target div below?

<div id="assembly_stats">
<script>
  d3.json("Danaus_plexippus_v3.assembly-stats.json", function(error, json) {
    if (error) return console.warn(error);
    asm = new Assembly (json);
    asm.drawPlot('assembly_stats');
  })
</script>

Below is the .html file I have. The .html file and Danaus_plexippus_v3.assembly-stats.json are in the same directory.

<html>
<head>
    <title>assembly stats</title>
  </head>
  <body>
    <link rel="stylesheet" type="text/css" href="css/circle-plot.css">
    <link rel="stylesheet" type="text/css" href="css/square-plot.css">
    <link rel="stylesheet" type="text/css" href="css/table.css">
    <script src="https://ajax.googleapis.com/ajax/libs/jquery/1.12.2/jquery.min.js"></script>
    <script src="https://d3js.org/d3.v3.min.js" charset="utf-8"></script>
    <script src="http://labratrevenge.com/d3-tip/javascripts/d3.tip.v0.6.3.js"></script>
    <script type="text/javascript" src="js/circle-plot.js"></script>
    <script type="text/javascript" src="js/square-plot.js"></script>
    <script type="text/javascript" src="js/table.js"></script>
    <div id="assembly_stats">
    <script>
      d3.json("Danaus_plexippus_v3.assembly-stats.json", function(error, json) {
        if (error) return console.warn(error);
        asm = new Assembly (json);
        asm.drawPlot('assembly_stats');
      })
    </script>
  </body>
</html>

Any help is greatly appreciated.

Using github pages to run assembly-stats

Hi there,

I hope this is okay to post here. If you are having trouble running assembly-stats checkout this fork which demonstrates how to run using github pages: https://github.com/ammaraziz/assembly-stats

Demo of it running here: https://ammaraziz.github.io/assembly-stats/

If there's interest I can write up a detail instructions on how to run assembly-stats on your own repo.

Thanks,

Ammar

Information on the compare tab

Hello, I'd like to know more about the comparison part. I find it very interesting to compare genomes. However, I didn't understand how you managed to display these results in the demo. Would it be possible to have more information please? Thank you in advance.

Are contig statistics visualized ?

Sorry, maybe it's a stupid question, but are contig statistics visualized ?
I can't find where are those statistics visualized in demo site.
http://content.lepbase.org/html/assembly-stats/assembly-stats.html?path=/v4/json/assemblies/&assembly=Danaus_plexippus_v3&view=circle&altAssembly=Danaus_plexippus_DanPle_1.0&altView=compare&altAssembly=Heliconius_melpomene_melpomene_Hmel2&altView=cumulative&altView=table

how to get the webpage

Dear Richard,

this looks fantastic. However, I am struggling to get my head around how to actually produce the page/ load the plots in my browser. I tried to have your code snippet

<div id="assembly_stats">
<script>
  d3.json("Danaus_plexippus_v3.assembly-stats.json", function(error, json) {
    if (error) return console.warn(error);
    asm = new Assembly (json);
    asm.drawPlot('assembly_stats');
  })
</script>

as an html file, but Firefox complains about the missing d3 object then.
Tried to add it like so

<div id="assembly_stats">
<script src="js/d3.js"></script>
 <script>

but then Firefox says there is an illegal character in d3. This is all done on an iMac. Also tested Vivaldi (Chrome) and Safari, no luck there.

Thanks

Philipp

Can not get the software work

I followed your documentation, and get the .json file ( let's call it output.json) by asm2stats.pl, but I don't the next step to visualize that output file, could you please give more info/guide about the detail after I get the .json file, thanks a lot

here is the script that I have tried:
file:///Users/myname/bin/assembly-stats/assembly-stats.html?path=/Users/myname/bin/assembly-stats/json/&assembly=output&view=circle&altView=cumulative&altView=table

btw, the plot from your software is really beautiful
best

Busco example

Hi:
Like many, I really like your output for genome visualisation.
I would like to add the BUSCOs for my genome, but I have copied/pasted the written example to include in the json file, and when I do, nothing shows up (even though before adding it the circular, cumulative and table were OK).
I was hoping if you could put up an example genome file with the buscos, the same way the Cegma is in the Danaus (as there is a particular way of writing it, with double quotes that are not shown in the text to paste).
Thanks again.

How to generate the plot and table?

HI, I'm actually trying to use your programm but I'm little vit stuck..
I already have generated the .jon file by doing:

And used this script:

<html>
<head>
    <title>assembly stats</title>
  </head>
  <body>
    <link rel="stylesheet" type="text/css" href="css/circle-plot.css">
    <link rel="stylesheet" type="text/css" href="css/square-plot.css">
    <link rel="stylesheet" type="text/css" href="css/table.css">
    <script src="https://ajax.googleapis.com/ajax/libs/jquery/1.12.2/jquery.min.js"></script>
    <script src="https://d3js.org/d3.v3.min.js" charset="utf-8"></script>
    <script src="http://labratrevenge.com/d3-tip/javascripts/d3.tip.v0.6.3.js"></script>
    <script type="text/javascript" src="js/circle-plot.js"></script>
    <script type="text/javascript" src="js/square-plot.js"></script>
    <script type="text/javascript" src="js/table.js"></script>
    <div id="assembly_stats">
    <script>
      d3.json("output.json", function(error, json) {
        if (error) return console.warn(error);
        asm = new Assembly (json);
        asm.drawPlot('assembly_stats');
        asm.drawTable('assembly_stats');
        asm.toggleVisible(['asm-longest_pie','asm-count']);
        
      })
    </script>

  </body>
</html>

But only the plot is here, there is not the table.

And also, I have busco output, how could I had these information into the plot?

Thanks for your help;

Missing contig length

After I trace the code, I see there is a missing value in contig statistics, which is at this line.

assembly-stats/js/circle-plot.js

Line 544 in 1f4e88e

    
           key.append('text').attr('x', w + 3).attr('y', w * 2.5 - 1).text('Contig length').attr('class', 'asm-key');

It should be something like this

assembly-stats/js/circle-plot.js

Line 518 in 1f4e88e

    
           key.append('text').attr('x', w + 3).attr('y', w * 2.5 - 1).text('Scaffold length (total ' + getReadableSeqSizeString(this.assembly, 0) + ')').attr('class', 'asm-key');

json output produced by asm2stat scripts not working

I am trying to generate the image using repo, however, it displays a blank white screen for jsons generated by either of the asm2stat scripts.

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