Answer: "in the sense a sample containing varying degrees of different bacteria"
You can also ask Ray to search for known things in the de Bruijn graph too. On Fri, 2012-03-30 at 21:59 -0400, Louis Letourneau wrote: > Congrats. > > > - Ray works on meta-genomes. > meta-genomes in the sense, multiple individual of the same genome (a-la > cortex) or in the sense a sample containing varying degrees of different > bacteria? > > Thanks > Louis > > On 3/28/2012 5:46 PM, Sébastien Boisvert wrote: > > Hello, > > > > Ray 1.7 was released on 2011-10-03, almost 6 months ago. > > > > We are proud to release Ray 2.0-Release Candidate 5. > > A release candidate is usually something quite stable. > > > > > > Summary of changes: > > > > New features: > > > > > > - A obvious peak in the coverage distribution is not required anymore. > > - Ray works on meta-genomes. > > - Reference sequences can be provided to do k-mer counting with a > > colored de Bruijn graph. > > - A taxonomic tree can be provided to perform taxonomic profiling using > > a distributed de Bruijn graph with virtual coloring. > > - A new output file contains contig neighbours. > > - A new directory called BiologicalAbundances contains biological > > abundances. > > - Ray can be compiled with CMake. > > - A header was added for scaffold links. > > - Contig are identified if reference sequences are provided via -search. > > - The speed is now shown in each step (like assembling at 5000 > > k-mers/second). > > - A new option can enable message routing for large jobs. > > - The algorithm that computes assembly seeds was modified to avoid > > assembly errors at this point. > > - Expiry positions for sequence reads are improved. > > - The file ElapsedTime contains the elapsed time. > > - Several options were added to debug assemblies. > > > > > > Code refactoring: > > > > - Test suites are in a distinct project. > > - Ray was ported to a new plugin architecture called RayPlatform. > > - The code that helps with content creation is now in RayPlatform. Ray > > ships with this. > > - The seed extension code was refactored. > > > > Tests: > > > > - New tests for peak calling for pairs of sequences. > > > > > > Bug fixes: > > > > - A bug that generated a segmentation fault in the virtual communicator > > in some very rare cases. > > > > > > > > To download Ray 2.0-Release Candidate 5: > > > > http://sourceforge.net/projects/denovoassembler/files/Ray-2.0-Release_Candidate_5/ > > > > > > > > > > > > Sébastien > > > > > > ------------------------------------------------------------------------------ > > This SF email is sponsosred by: > > Try Windows Azure free for 90 days Click Here > > http://p.sf.net/sfu/sfd2d-msazure > > _______________________________________________ > > Denovoassembler-users mailing list > > Denovoassembler-users@lists.sourceforge.net > > https://lists.sourceforge.net/lists/listinfo/denovoassembler-users > > ------------------------------------------------------------------------------ > This SF email is sponsosred by: > Try Windows Azure free for 90 days Click Here > http://p.sf.net/sfu/sfd2d-msazure > _______________________________________________ > Denovoassembler-users mailing list > Denovoassembler-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/denovoassembler-users ------------------------------------------------------------------------------ This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure _______________________________________________ Denovoassembler-users mailing list Denovoassembler-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
