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Old 08-25-2010, 02:46 AM   #1
smice
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Exclamation GenoViewer: a new next generation sequencing viewer/browser is available now!

GenoViewer, the latest software developed by Astrid Research, Inc., is now available.

By developing GenoViewer, our aim was to develop a user-friendly viewer for NGS assembly data visualization, which is able to natively read SAM/BAM format. We realized the need for a viewer that can read the mentioned universal format produced and processed by most free software tools, usually huge in size and rich in information, but hard to view, manage and understand. We would like to help the NGS community with our innovative visualizing tool.

You can read more about the GenoViewer at its website, where you can also download it for free:

www.GenoViewer.com

The product also has a version that loads a sample dataset instantly. Remember that the application is under constant development, many features are still to come. New versions will be announced frequently, so do not forget to check back regularly (we recommend utilizing the RSS feed).

We focus on:
  1. Helping you. Feel free to download and work with GenoViewer. If you have questions, contact us and we will be glad to assist you.
  2. Improving our product. Let us know your comments and questions. We appreciate positive and negative feedback alike.


Highlight features:
  • Loading really huge files, practically there is no limit for BAM files
  • Reading SAM/BAM files for assembly, FASTA formats for reference sequence, GFF files for annotation
  • Displaying every important bases/colours: read errors, SNPs, MNPs, insertions, deletions
  • Works in colour space as well as base space
  • Mutation table generation and export
  • Easy to overview, but no loss of information: details for every read
  • Easy navigation and zooming, with hotkeys, mouse, or GOTO/search options
  • Workspaces and project folders to organize your work
  • Fully personalizable displaying profiles
  • User friendly environment

Thanks for supporting us with downloads and comments!
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Old 08-25-2010, 05:39 AM   #2
maubp
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When run on Mac OS X the menu is in the wrong place (should be at the top of the screen, instead it is embedded in the application window).

Also the zoom in keyboard commands don't work (expected Apple+Plus, Apple+Minus - I also tried using control, and both the +/- on the main keyboard and on the numberpad).

Clicking on the alignment brings up a floating window with the alignment information for that read. However, this window floats on top of all other windows - even if I switch to a different application such as my webbrowser.

It doesn't appear to let me drag the view using the mouse (except by using the scroll bars). Mouse wheel/ball scrolling doesn't work either.

Left and right cursors work for panning, but not up and down.

Picard gives a validation error from the example BAM file, is this information shown anywhere:
Quote:
SAM validation error: ERROR: Record 1, Read name 1876 Example sequence FW - secondary sequence 3, MRNM should not be set for unpaired read.
On a positive note, I do like the way it shows the pairwise alignment between the reference sequence and the selected read. This is useful to visualise inserts (marked by a small pink bar on the main display).
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Old 08-25-2010, 06:00 AM   #3
maubp
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Quote:
Originally Posted by smice View Post
Highlight features:
  • Loading really huge files, practically there is no limit for BAM files
I've just tried it on a couple of different 2.5 GB BAM files containing paired end Illumina transcriptome reads mapped onto a draft assembly of about 80,000 contigs/scaffolds. I waited well over an hour, and gave up. GenoViewer was using 32 threads, but only 2% CPU.

Even if it did load these files, I am curious about how the contig selection would work. A single drop down menu listing the contigs is a bad idea once you have more than a dozen reference sequences.

(For comparison, Tablet can load these BAM files in about six seconds)

Last edited by maubp; 08-25-2010 at 07:54 AM. Reason: Update after trying to load test files
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Old 08-25-2010, 08:02 AM   #4
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Here is a public example that GenoViewer 0.9.0beta doesn't seem to load, its from the BamView documentation at http://bamview.sourceforge.net/

Plasmodium falciparum reference sequence:
ftp://ftp.sanger.ac.uk/pub/pathogens...ce.2.1.4.fasta

390MB BAM file and its index:
ftp://ftp.sanger.ac.uk/pub/pathogens...3D7_RNASeq.bam
ftp://ftp.sanger.ac.uk/pub/pathogens...RNASeq.bam.bai

GenoViewer could load the FASTA file fine, but doesn't seem to like the BAM file - I just get the blue progress bar/spinner.

Last edited by maubp; 08-25-2010 at 08:05 AM. Reason: Added file size
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Old 08-25-2010, 08:04 AM   #5
maubp
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Bug report: On Mac OS X, the "About" screen says it is version 1.0, not 0.9.0b.
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Old 08-26-2010, 06:58 AM   #6
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Dear maubp!

Thank you for your remarks. Note that the software is a beta version and is still under development, some features are not working seamlessly and many features will be added in the near future. Our aim with making it available publicly before it is 'finished' was to gather ideas from the users themselves directly, and discover bugs that are not so obvious for software developers (for example, we did not tested of loading files containing 80.000+ contigs, we never thought it is needed). And you are a great help in that.

Many things you mentioned are already among our planned features (like the screen dragging with the mouse). I am considering of adding a page to the GenoViewer site that describes the features we are working on/planning, so that everyone can see them.

- About the version number bug, it's a mystery, we couldn't reproduce it. The version number appears correctly when we use the downloadable version.

- About the BAM files you couldn't open: it's not because the size. Size doesn't matter, because when the viewer loads the file, it only keeps a fixed part in the memory, instead of trying to load the whole file. That's why there is no size limit, theoretically. The reason behind not opening these files is most likely related to the many contigs they contain. We are aware of this, and we are working on it; redesigning the contig selection method too. Top priority for us. Maybe you could tell us, what would you like to see for navigation among 80.000+ contigs.

- Currently the functioning navigation keys (as you wrote): left and right arrow for horizontal scrolling, mouse wheel for vertical scrolling, numpad + and - for zooming (without Ctrl or Apple keys). Further keys and features are planned (like vertical arrow keys and mouse ball supporting, screen dragging).

- The software is JAVA-based, which is platform independent. It should work properly, no matter what OS you use. It's a pity that the menu is appearing on the wrong place on your Mac, we are checking it.

Thank you for the feedback!
There will be a new release available on www.GenoViewer.com soon!
We are working to fix the problems you noted.

Last edited by smice; 08-26-2010 at 07:05 AM.
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Old 08-26-2010, 08:01 AM   #7
maubp
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Quote:
Originally Posted by smice View Post
Dear maubp!

Thank you for your remarks. Note that the software is a beta version and is still under development, some features are not working seamlessly and many features will be added in the near future. Our aim with making it available publicly before it is 'finished' was to gather ideas from the users themselves directly, and discover bugs that are not so obvious for software developers (for example, we did not tested of loading files containing 80.000+ contigs, we never thought it is needed). And you are a great help in that.
No problem
Quote:
Many things you mentioned are already among our planned features (like the screen dragging with the mouse). I am considering of adding a page to the GenoViewer site that describes the features we are working on/planning, so that everyone can see them.
That would be a good idea.
Quote:
- About the version number bug, it's a mystery, we couldn't reproduce it. The version number appears correctly when we use the downloadable version.
I understand why now:

If I use the "Help, About" on the menu within the application window, then I see 0.9.0b

If I use the Apple standard menu at the top of the screen, then I see 1.0 - Perhaps this coming from another source of information?
Quote:
- About the BAM files you couldn't open: it's not because the size. Size doesn't matter, because when the viewer loads the file, it only keeps a fixed part in the memory, instead of trying to load the whole file. That's why there is no size limit, theoretically. The reason behind not opening these files is most likely related to the many contigs they contain. We are aware of this, and we are working on it;
What about the plasmodium example? That only has about a dozen reference sequences?
Quote:
redesigning the contig selection method too. Top priority for us. Maybe you could tell us, what would you like to see for navigation among 80.000+ contigs.
BamView and the Artemis plugin version have the same problem, they also use a drop down list.

I like the table used in Tablet, http://bioinf.scri.ac.uk/tablet/
Quote:
- Currently the functioning navigation keys (as you wrote): left and right arrow for horizontal scrolling, mouse wheel for vertical scrolling, numpad + and - for zooming (without Ctrl or Apple keys). Further keys and features are planned (like vertical arrow keys and mouse ball supporting, screen dragging).
Yes you are right - using the number pad keys plus, minus and multiply on their own do work. I was puzzled by the icon shown on the menu for the keyboard shortcuts though (is it a numberpad?).

I would still encourage you to support platform zoom conventions as well (or instead). For example most web browsers use Apple or Control with plus and minus and zero for zooming in, out and resetting the view.

Also note not all keyboards come with a dedicated number pad - Apple certainly ship small keyboards with some machines.
Quote:
- The software is JAVA-based, which is platform independent. It should work properly, no matter what OS you use. It's a pity that the menu is appearing on the wrong place on your Mac, we are checking it.
I think this happens by default with JAVA software on the Mac, you have to handle this explicitly to follow the Mac GUI conventions.
Quote:
Thank you for the feedback!
There will be a new release available on www.GenoViewer.com soon!
We are working to fix the problems you noted.
Great.
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Old 08-26-2010, 08:40 AM   #8
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You're missing the best bit though... the "actual size" button!

That made me chuckle a little bit. I assume it's just due to using some standard toolkit components, but obviously the actual size for DNA would be far far smaller than what you display. :-) Renaming the tooltip to something else resolves this minor amusement.

As for loading causing problems even with just a few references/contigs, my guess is it's a failure in something like picard not being handled properly. Are there options to tell picard to be lenient or silent when opening the BAM file? Otherwise a lot of BAMs will get rejected.

Anyway, it's good to see lots of choice of viewers.
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Old 08-26-2010, 09:01 AM   #9
maubp
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Quote:
Originally Posted by jkbonfield View Post
You're missing the best bit though... the "actual size" button!

That made me chuckle a little bit. I assume it's just due to using some standard toolkit components, but obviously the actual size for DNA would be far far smaller than what you display. :-) Renaming the tooltip to something else resolves this minor amusement.
Yeah, call it "Reset zoom" or something instead.
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Old 08-30-2010, 01:09 PM   #10
maubp
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There is some more feedback here - I'd agree the current colours are quite garish:
http://jermdemo.blogspot.com/2010/08...-reviewed.html
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Old 08-30-2010, 05:49 PM   #11
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Here is my review:

http://lh3lh3.users.sourceforge.net/NGSalnview.shtml

It is a little old; not including GenoViewer unfortunately.
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Old 09-01-2010, 06:24 AM   #12
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lh3, that's a great comprehensive review, would you update it and include GenoViewer?

Well, "actual size" button has been renamed, you were right. It wouldn't be so useful assembly viewer if it would display an actual genom, in its actual size. I liked jkbonfield's comment. By the way, actual size means the view where a 16 dot letter is 16 dot indeed on the display, it was merely about that. But I agree, it wasn't a very good name.

The eye hurting colours are good for quickly pointing out the differences among the sequences. Besides, in the Profiles menu, you can choose from more than 16.7 million distinct colours, plus shades etc., effectively the whole 32 bit colour range is available, and lots of different profiles can be created and saved, so I hope it satisfies everyone's taste. Nevertheless, the default colours are redesigned.

We are working on the Mac problems, like the version number (we have discovered the reason, too) and the menu problems. It will take a while to fix it.

The plasmodium files contain 16 contigs, do they? I think everything with more than 10 contigs is too much for the downloadable version. The current version we have though has already overcome the problem, it should open the 80,000 contig file, or any file. I am eager to here about it! It will be available on the site soon.
However, redesigning the contig selection method takes more time, so until it is finished we still use the drop down menu, where you can choose from a limited amount of reference contigs and assembly contigs. The limit is 20. (So you will be able to open any file, but if it contains more than 20 contigs, you will only see the first 20.)

The hotkeys are also reconsidered. We are aware that NumPad is not available everywhere (laptops quite rarely have it, for example).

Quote:
Yes you are right - using the number pad keys plus, minus and multiply on their own do work. I was puzzled by the icon shown on the menu for the keyboard shortcuts though (is it a numberpad?).
I don't get this part - the menu says 'NumPad +'. Yes, NumPad means Number Pad. Is it confusing? Maybe you ran into another Mac related problem?

Thanks for the advices!
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Old 09-01-2010, 06:37 AM   #13
maubp
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Quote:
Originally Posted by smice View Post
I don't get this part - the menu says 'NumPad +'. Yes, NumPad means Number Pad. Is it confusing? Maybe you ran into another Mac related problem?

Thanks for the advices!
Probably a Mac issue - I didn't see the words "NumPad" but an icon which represented the number pad.
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Old 09-01-2010, 06:41 AM   #14
maubp
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Quote:
Originally Posted by smice View Post
The plasmodium files contain 16 contigs, do they? I think everything with more than 10 contigs is too much for the downloadable version. The current version we have though has already overcome the problem, it should open the 80,000 contig file, or any file. I am eager to here about it! It will be available on the site soon.
However, redesigning the contig selection method takes more time, so until it is finished we still use the drop down menu, where you can choose from a limited amount of reference contigs and assembly contigs. The limit is 20. (So you will be able to open any file, but if it contains more than 20 contigs, you will only see the first 20.)
If you have to have a limit in the short term just 20 seems too tight. Humans have 22 chromosomes plus the X/Y, and mitochondria. How about 50 or 100?
http://en.wikipedia.org/wiki/List_of...ious_organisms

Last edited by maubp; 09-01-2010 at 06:52 AM. Reason: typo
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Old 09-17-2010, 06:12 AM   #15
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We have just uploaded a newer version to the GenoViewer site. Please check it out, it contains various fixes and the annotation management is also redesigned (the change perhaps not so spectacular but hopefully it handles much more non-standard GFF files).

Also, we will present our work in the poster section of the Next-Generation Sequencing Data Management conference held in Providence, Rhode Island (September 27-29). Meet us there if you feel like!
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Old 09-19-2010, 04:01 AM   #16
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Default the viewer for 454?

Does this viewer fit 454 data?
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Old 09-19-2010, 11:10 PM   #17
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Yes, of course. The viewer is designed to visualize assembly data stored in SAM/BAM files, no matter where the data came from, what kind of sequencing technology you used. Although note that the colour code related features won't work, naturally.
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Old 09-19-2010, 11:17 PM   #18
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Default 454

Yes, but in 454 we do not have SAM/BAM output...
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Old 09-19-2010, 11:32 PM   #19
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What kind of assembly software do you use? I assume its output can be converted to SAM/BAM. The file format itself of the SAM/BAM does allow the use of 454 reads, so technically it is undoubtedly possible.
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Old 09-20-2010, 02:26 AM   #20
maubp
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I've just downloaded and tried GenoViewer 0.9.0-0003
Quote:
Originally Posted by maubp View Post
If I use the "Help, About" on the menu within the application window, then I see 0.9.0b

If I use the Apple standard menu at the top of the screen, then I see 1.0 - Perhaps this coming from another source of information?
That is fixed in 0.9.0-0003

I just tried the Plasmodium example again, and it loads now. I loaded the BAM file on its own, and everything seemed fine. Then I loaded the FASTA reference as well, then I could see all the contigs listed twice under the contig menu -- this is odd
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