GenoViewer: a new next generation sequencing viewer/browser is available now!

[maubp]

There is some more feedback here - I'd agree the current colours are quite garish:

http://jermdemo.blogspot.com/2010/08/ngs-viewers-reviewed.html

[maubp]

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.

[jkbonfield]

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.

[maubp]

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

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.

- 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?

- 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?

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/

- 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.

- 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.

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.

[smice]

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.

[maubp]

Bug report: On Mac OS X, the "About" screen says it is version 1.0, not 0.9.0b.

[maubp]

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.

[maubp]

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)

[maubp]

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:

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).

[smice]

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!