Welcome, Guest. Please Login or Register
UGENE Bulletin Board
  Welcome to our forum.
  HomeHelpSearchLoginRegister  
 
 
Page Index Toggle Pages: 1
DNA assembly tool (Read 10527 times)
Jun 2nd, 2010 at 10:47pm

josecolquitt1   Offline
YaBB Newbies

Posts: 2
*
 
There are two assembly options when using the DNA ass. tool.  Does the bowtie option use the Burrows-Wheeler algorithm to align the short reads to the give reference?

Also is there any explanation/documentation on the UGENE genome aligner option also available in the DNA assembly tool?  Thank you in advance
 
IP Logged
 
Reply #1 - Jun 3rd, 2010 at 1:18pm

Konstantin Okonechnikov   Offline
Global Moderator

Posts: 173
*****
 
In version 1.7 of UGENE there are 2 algorithms for DNA to reference assembly available.

And, yes, you're right, the first one is port of Bowtie tool, which uses the Burrows-Wheeler based index. If you have a built index, you can use it as reference sequence. Read more about Bowtie here.

The genome aligner tool is based on unique algorithm developed by UGENE team. There is a documentation page available. It's not much, still you might find it helpful.

If you need more information on genome aligner tool or dna assembly usage, we'll be glad to answer your questions.
 
IP Logged
 
Reply #2 - Jun 7th, 2010 at 10:45pm

josecolquitt1   Offline
YaBB Newbies

Posts: 2
*
 
Thank you.  Are there any plans to add more options to the DNA assembler such as a greater allowance for mismatches?  I have completed alignments using both the UGENE unique alignment algorithm and the bowtie option for a current projetct, yet some of the longer reads that I am currently working with are omitted due to the setting. 

Just a thought.
 
IP Logged
 
Reply #3 - Jun 8th, 2010 at 12:32pm

Konstantin Okonechnikov   Offline
Global Moderator

Posts: 173
*****
 
Thanks for the suggestion!

Actually, we're planning to support mismatch rate up to 5% of reference sequence length in next releases.
For Bowtie maximum allowed mismatch number is 3 (as it is pointed in the manual)  
 
IP Logged
 
Reply #4 - Sep 9th, 2010 at 3:50pm

Edward Oakeley   Offline
YaBB Newbies

Posts: 2
*
 
Sorry for being slow/stupid but I am really struggling with this plugin. I have 30 million reads from a GAIIx as a Gerald file (s1_sequence.txt). I have the human pre-built index for Bowtie from their webpage (also tried making my own indexes from FASTA).

If I load the index as shown (click on the ewbt file 1) and I load the reads into the "add" panel and click start assembly the application crashes. I have tried on Windows 7-64bit (CUDA-enabled), Ubuntu 10.04-64bit, Mac OSx snow leopard. All show the same behaviour.

Can someone who got it to work give me a clue what I might be doing wrong?

Thanks
 
IP Logged
 
Reply #5 - Sep 9th, 2010 at 6:10pm

Edward Oakeley   Offline
YaBB Newbies

Posts: 2
*
 
I also tried converting all the reads from fastq/gerald to fasta (removing quality line and header and replacing @ with >). This also crashes the program. See attached file...
 

error.jpg (100 KB | )
error.jpg
IP Logged
 
Page Index Toggle Pages: 1