454 software installation

[kchen]

Greetings NGS Community,

I am very new to next generation sequencing in particular to the analysis of large scale sequencing data. I have got a full plate of 454 sequencing data with the .sff files, but I need 454 software to output the .sff.txt files. I would like to ask if the NGS friends here could possibly tell me whether the package of 454 sequencing analysis tools would be able to be run in a macintosh computer or not. It seems to me in the instruction that the package of 454 sequencing analysis tools are currently only supported on Linux platforms running on 32-bit or 64-bit x86 architecture. Many thanks!

K

[flxlex]

Linux only, not suited for Macintosh, I'm afraid...

[Palecomic]

You could run it in virtualbox though - Qiime for microbial ecology requires the sfftools from 454 for some of its functionality and runs nicely in VirtualBox, transferring files back and forth easily using a shared folder.

http://qiime.sourceforge.net/install/virtual_box.html

[kmcarr]

If your only need is to extract text files (fasta & qual) from the .sff files you can do this with sff_extract. This program is written in Python and will run on your Mac.

[Cansado]

How to install Roche 454 software in Qiime Virtual box?

Hi:

Tried to install Roche 454 software in Qiime Virtual box?
Two problems:
1) system install has this error:
"One or more of the following libraries was not found
zlib.i386, libXi.i386, libXtst.i386, libXaw.i386"
2) root library password required.
Is the Qiime Virtual box root password available?

Can anyone help with these issues?

Thanks

(BTW, trying to use Roche 454 software on Mac and following recommendation to try Qiime Virtual box to emulate the Linux environment)

[Cansado]

Installed Roche 454 software in Qiime Virtual box!

OK. Figured out after seeing "Newbler installation" on Ubuntu forums:
http://ubuntuforums.org/showthread.php?t=1624351

The basic answer is to type this in terminal:
sudo apt-get install ia32-libs

Apparently, need to install 32-bit libraries and dependencies.

I installed as "Local" and did not need root library password.
Apparently Qiime does not appear to have a root password.

Cheers

[Palecomic]

I'm fairly sure the virtual box root password used to be 'qiime', but that may not be the case in the most recent version.

If you're using qiime on a mac, save yourself effort by installing macqiime from Jeff Werner http://www.wernerlab.org/software/macqiime it works like a dream and installs very simply. It will work faster than the virtualbox on the same machine as it's native. He does a good job of keeping up with the main Qiime releases too!

Also qiime 1.3 has a python script for .sff to .fna and .qual http://qiime.sourceforge.net/scripts...hlight=sffinfo I think I read that they're a little slower than sffinfo, but in case someone doesn't want to or can't install sfftools

[Cansado]

Thanks Palecomic:

Right, qiime could be the root password. I used that during the Qiime virtual box additions update. However, did not need it once the needed libraries and dependencies were installed for the 454 software install.

Don't know anything about Qiime. Should I use this instead of the 454 software tools? We just received some 454 files and thought to try the same software that they used. In any case, I have a learning curve ahead...

Cheers

[Palecomic]

What's your application? Qiime is for 16S rRNA amplicon sequencing or other microbial ecology stuff.

[Cansado]

Immunology. IGHV amplicon. Assessing mutation rate.
What do you think?

[Palecomic]

I would guess not, though there might be some useful aspects of it? I think you might need a friendly local bioinformatician to help get you started.

[Dicius]

Qiime VirtualBox password change

I don´t know the password, and in my case "qiime" didn´t work...

But I discovered, that running command:

sudo passwd root

which will prompt you to set a new password...

[elizondas]

I have just installed qiime and I am asked for a password when I am typing the command Vboxaddition. Anyone know something about it/