Also, this could mean that ray could now be used for transcriptome assembly then.
interesting. Louis On 12-04-02 09:42 AM, Sébastien Boisvert wrote: > 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
