Novoalign V2.0 Released

[sparks]

Hi,
Just let you know that Novoalign V2.0 is now available for download from www.novocraft.com.

This release has improved the accuracy of the quality scores for alignments. This has been done by extending the search space well
beyond the best alignment. There is no performance penalty.

Performance has also been improved for reference sets with a large number of sequences. There's a few other change documented in the release notes.

Happy New Year,
Colin

[doxologist]

Have this been benchmarked with software such as SOAP, MAQ, Eland, or Bowtie?

[zee]

We have been doing constant benchmarking since beginning of development of this tool. Novoalign has been compared with all the abovementioned tools as well as others such as rmap, razers, etc.
Check out http://www.novocraft.com/wiki/tiki-v...desc&forumId=5 for what's been done so far with maq.
We're preparing more data for a publication.

[doxologist]

thanks. unless I'm missing something, the link you posted is to a release announcement and not a comparison/benchmark.

[sparks]

Hi Doxologist,
We're preparing a paper that compares these tools on simulated data and should have it ready to submit in a week or so. Once the paper is out I will put some of this data on our web site.
Run time performance is similar to MAQ, not as fast as Bowtie. Accuracy is better as we do indels even on single end and our seeding algorithm isn't limited to two mismatches. Our paired end mode also has some advantages.
Colin

[doxologist]

thank you for the reply. that's most helpful. I look forward to your paper.

[mkatari]

a reference

Hi, I have used novoalign and would like to reference it in a grant i'm writing. Can you give me the authors and the title ? or should I just reference the website.
Thanks,

[sparks]

Hi mkatari,

At the moment we don't have any publications you can reference, we have submitted one but it's not out yet. I suggest you reference the web site.

If you are applying for a grant perhaps you would like to get a full license with support and access to additional features such as multi-threading. You can send a request for a quote via our contact form on the web site.

Best Regards, Colin