SeqAn – BioStore Conference 2014

17. April 2014

We invite you to the SeqAn – BioStore Conference 2014, June 11th -12th in Berlin, which at the same time is the final meeting of the VIP BioStore project.
The detailed information you can find on our BioStore website.

KNIME Workflows with SeqAn

27. March 2014

Dear SeqAn community,

We are happy to announce that we recently went into the KNIME Community Contributions. It is now easily possible for everyone to create, share and use workflows with SeqAn apps and create new SeqAn apps and integrate them into KNIME. In a few steps you can set up KNIME and integrate the SeqAn nodes update site. For now, we will host example workflows on github and are happy to integrate your workflows as well. Feel free to play and send us comments.

Cheers,
your SeqAn team.

SeqAn’s repository is migrating to GitHub

20. November 2013

The SeqAn team is migrating SeqAn’s repository to GitHub (SeqAn’s repository on GitHub). For the last months, we have already mirrored the Subversion trunk to the master branch at GitHub and worked on some larger changes there on the branch “develop”. Git allowed us to maintain multiple branches much easier than Subversion.

We have now decided that it is easier to continue development on GitHub. Thus, instead of copying over the changes from our Subversion trunk to GitHub, we will now copy over the changes in the GitHub master to the Subversion trunk.

One more thing: Everything else remains the same, i.e. http://packages.seqan.de still hosts our packages, http://trac.seqan.de remains our wiki, http://trac.seqan.de/wiki/Tutorial contains the Tutorial, http://docs.seqan.de is still there for our documentation.
What does this mean for you?

SeqAn SVN Users

You just use SeqAn in your projects and get the latest version from SeqAn’s trunk? No problem, we will continue pushing the changes from the stable Git master to SeqAn’s trunk. The SeqAn SVN URL stays the same. You even have the added benefit that the new trunk will be more stable since the development will happen in different branches on GitHub. Yay!

Did you know that you can also checkout GitHub repositories via Subversion? Thus, you could also use the develop branch at Github to get the lastest (albeit less stable) SeqAn version:

svn co https://github.com/seqan/seqan/branches/develop seqan-trunk

SeqAn Tarball Users

You use the SeqAn library from a downloaded tarball or one of our applications? Nothing changes for you.

SeqAn Contributors

You are contributing to SeqAn or you want to? It’s now much less hassle to do so! GitHub allows you to easily submit patches through pull requests which we can then review and merge.

More information on how we use Git and links to tutorials online can be found at in our How-To: Use Git.

tl;dr We are moving to Git. Don’t worry if you are using tarball downloads or just read from our Subversion repository — nothing changes for you.

NVIDIA CUDA Research Center

18. November 2013

The Algorithmic Bioinformatics Group at the Freie Universität Berlin is now a CUDA Research Center with SeqAn in its focus.
For more information about the NVIDIA research program please visit the new centers blog announcement.

GTC Express Webinar: Introduction to SeqAn

22. October 2013

Prof. Dr. Knut Reinert and Dr. David Weese presented SeqAn at the GPU Technology Conference Express Webinar and showed how GPUs can be used with SeqAn to generically accelerate algorithms for biological sequence analysis.
You can download the video and the slides.

SeqAn – BioStore Workshop 2013

15. July 2013

This year’s SeqAn – BioStore Workshop 2013 will take place in September 17th -19th in Berlin.
More information you can find on our BioStore website.

SeqAn Release 1.4.1

11. July 2013

The SeqAn team is happy to announce the 1.4.1 release of the SeqAn apps and libraries. This update includes some new features and bug fixes over the 1.4.0 release and should be compatible otherwise.

You can download the release packages at http://packages.seqan.de.

The highlights are:

  • many new demos and improved API documentation throughout the library and for central classes, and
  • new file format support and tutorials for this: VCF, BED, GFF.

We recommend everyone to upgrade to the new version.

You can find a more extensive list of changes in the change log.

Enjoy!
The SeqAn Team

SeqAn Release 1.4

29. April 2013

The SeqAn team is happy to announce the 1.4 Release of the SeqAn apps and libraries. This update includes all improvements and changes over the last two years since the 1.3 release. You can download the release packages at http://packages.seqan.de.

Some highlights are:

  • New read mapping programs Masai (backtracks two string tries in parallel) and RazerS 3 (uses q-gram index filters and OpenMP).
  • An efficient implementation of an FM index that combines good performance with low memory usage and can be iterated as a prefix trie via the string tree iterator interface
  • A new command line parser that facilitates the integration of programs into workflow engines such as KNIME or Galaxy.
  • An extended and more robust I/O system, namely in the modules seq_io, gff_io, bam_io.

You can find a list of many more updates in our Trac wiki in the Changelog.

If you are upgrading from a previous release, you can learn about the new library content in the updated tutorial.

In case of questions or support, please send an email to our mailing list.

Have fun!
The SeqAn Team

SeqAn Seeds Update

13. March 2013

The SeqAn team is happy to announce the update of the seeds module.

The previous seeds module had numerous problems, including memory leaks and bugs. We have rewritten the seeds module such that it now supports a more handy interface while removing the bugs and the problems of the previous one. The new version is based on the interim module seeds2. We have adapted the interfaces to better match the contents of the whole library, especially with the updated alignment module.

The new seeds module features:

  • A basic implementation of the SeedSet class. A more refined version will follow shortly.
  • An updated interface for the Seed class for local chaining and its specializations.
  • An updated version of the global chaining algorithm.
  • A greatly updated and improved version of the banded chain alignment module based on the new alignment module.

The API documentation has already been updated to provide documentation for the new module. We are currently in the process of  updating the Seed-and-Extend tutorial.

We are certain that the updates are a great improvement over the old seeds module and hope that the update does not cause too much inconvenience.

Have fun with the new seeds module!

SeqAn Subversion Repository Moved

4. October 2012

The SeqAn subversion has moved. The path of the trunk moved from http://svn.mi.fu-berlin.de/trunk/seqan/trunk to http://svn.seqan.de/seqan/trunk.

The new repository is a bit more sorted and the repository is now world-readable (without any path-based access control that gave troubles in the past).

To update to the new repository path, please create a fresh checkout of http://svn.seqan.de/seqan/trunk.