[litali]

the viewer for 454?

Does this viewer fit 454 data?

[smice]

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.

[litali]

454

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

[smice]

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.

[maubp]

I've just downloaded and tried GenoViewer 0.9.0-0003

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

[maubp]

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.

[smice]

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.

[maubp]

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:

http://seqanswers.com/forums/showthread.php?t=6557

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?

[smice]

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!

[maubp]

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