Hi, We did some tests on Schizosaccharomyces pombe data from the Trinity paper.
It was good, but I don't know if it compares well with other established methods (i.e. Trans-ABySS or Trinity). By good, I mean about 1 contig per transcript, sometimes 2. And there were apparently a lot of other contigs that were adapter-related I think. With the biological abundance feature, you get k-mer coverage distribution for each contigs as well as biological functions of contigs if the corresponding reference was provided via the -search command. So it is akin to a virtual microarray experiment wherein the probes are k-mers, and you also get assemblies. But right now, we are working on the microbiome metagenomes. If you like software design and runtime stuff, you will also find keen interest in the RayOutput/Scheduling/ and RayOutput/Plugins/ directories, which contain runtime information. We are proud of the new "kernel-like" design. This design enabled us to add lots of code to Ray in a modular way ! On Mon, 2012-04-02 at 09:45 -0400, Louis Letourneau wrote: > 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
