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

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.

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.

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)  

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

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...

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