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  • maubp
    replied
    I suggest you ask one of your former colleagues to subscribe to this thread, especially as the blog suggests people get in touch here.

    Leave a comment:


  • smice
    replied
    Hello, I am no longer working for the company developing the GenoViewer (Astrid Research Inc.), so I cannot speak in their name. When I left there was a clear intention to finish it (as you see, it still has not reached version number 1), but when will it happen I don't know, since it became a lower priority project.

    For in-house use we had an improved version, which contained a lot of new features, including the ones discussed here (like advanced multicontig management), but that has not been released yet because it's not properly tested and debugged (because of change of project priority before release).

    I can't tell when it will be high priority again, but I can give you a contact e-mail address or ask one of my former colleagues to answer your question here on SEQanswers. I hope the development will continue soon though, I know a manuscript about GenoViewer is currently submitted and under review.

    Thanks for inquiring!

    Leave a comment:


  • maubp
    replied
    Are you still working on this? The latest blog posts on http://www.genoviewer.com/wordpress/ are:

    No Comment
    February 24, 2011

    Due to the flood of spams commenting is currently not available on this site. If you would like to discuss GenoViewer, please write an email to the contact address or visit the SEQanswers forum:

    Discussion of next-gen sequencing related bioinformatics: resources, algorithms, open source efforts, etc


    Thank you, and sorry for the incidental inconveniences!
    Future features update
    October 12, 2010

    Recently the development has been held back, but now it is given full throttle again! We plan to release a new version soon. We’ve already handled these issues:
    • Annotation redesigning
    • Multicontig file handling
    • Mac problems
    • Sequence based search
    • Extended use of the side panel
    • Mutation table sorting


    Check out the Future features page to see what we are currently working on!
    However, the current download is still 0.9.0-0003 which was released in September 2010. What happened to the work from October 2010?

    Leave a comment:


  • smice
    replied
    That is because you can select different contigs from the fasta file and different contigs from the BAM file. The upper ones change the reference, the lower ones, below the separating line, change the reads aligned. I know it is not a very good solution but this is temporary, a better design will be ready soon. (A searchable, scrollable list on the side panel, listing all of the contigs, the reference and the assembly alike, but on different panels.)

    Because not everyone uses a fasta file corresponding exactly to the assembly file, it is necessary to choose between the contigs of both.
    Last edited by smice; 09-20-2010, 03:30 AM.

    Leave a comment:


  • maubp
    replied
    Originally posted by litali View Post
    Yes, but in 454 we do not have SAM/BAM output...
    According to second hand information (i.e. rumors), Roche are working on adding SAM/BAM output to their "Newber" gsAssembler.

    Leave a comment:


  • maubp
    replied
    I've just downloaded and tried GenoViewer 0.9.0-0003
    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

    Leave a comment:


  • smice
    replied
    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.

    Leave a comment:


  • litali
    replied
    454

    Yes, but in 454 we do not have SAM/BAM output...

    Leave a comment:


  • smice
    replied
    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.

    Leave a comment:


  • litali
    replied
    the viewer for 454?

    Does this viewer fit 454 data?

    Leave a comment:


  • smice
    replied
    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!

    Leave a comment:


  • maubp
    replied
    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?
    Last edited by maubp; 09-01-2010, 06:52 AM. Reason: typo

    Leave a comment:


  • maubp
    replied
    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.

    Leave a comment:


  • smice
    replied
    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).

    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!

    Leave a comment:


  • lh3
    replied
    Here is my review:



    It is a little old; not including GenoViewer unfortunately.

    Leave a comment:

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