EULER Portal

http://euler-assembler.ucsd.edu/euler-sr.1.1.2.tgz

In the release:

- Fixed a memory "leak" where c++ vector wasn't releasing cleared memory.

- Made graph simplification sequence specific and not just topology specific.

- Fixed graph simplification to use fewer iterations (faster).
- Modified command line usage to allow manual specification of the minimal k-mer multiplicity (skips error correction... this often gives the same result as with error correction, but 10 times faster using more memory).

Release 1.1 is posted. Use the link here instead of logging on to download.

If you are downloading the x86_64 binaries, they run on Ubuntu 8.04, and there are problems on other architectures/OSes. Please compile the source on other systems.

Feelfree to circumvent the download page for now: http://euler-assembler.ucsd.edu/euler-sr.1.0.tgz

Updates to the web page (and responses to e-mail) will be slow until Jan 25 since I will be traveling.

The portal will be briefly going offline on Dec. 24 for maintenance.

A release has been posted that fixes a core dump in the preprocessing phase. This is a necessary upgrade.

Our publication on EULER-USR (Ultra-short read assembler) has been released on advance online publication:

The drive with the site crashed, so I'm restoring it. All functionality should return within a day.

The first update fixes some compile issues people had on non x86_64 architectures, and made the regular expression syntax use the POSIX extended format for easier regexp matching.