Hello,
There is the Documentation/ directory that contains documentation. Also: Ray -help|less The new RayOutput/BiologicalAbundances/ directory contains, for example, detailed information for each contig, as is. You can also search for sequences. Just put the fasta sequences you want to search in the de Bruijn graph in a directory and run Ray with: mpiexec -n 99 Ray -p 11.fastq 12.fastq -search directoryWithSequences This is documented in Documentation/BiologicalAbundances.txt in the distribution. You can also provide a taxonomy (like the NCBI taxonomy or, the more accurate Greengenes taxonomy). There is some file conversion to do for the taxonomy features. This is documented in Documentation/Taxonomy.txt This generates XML files inside RayOutput/BiologicalAbundances. These XML files have to be converted with XSL files, which are shipped with the distribution. We are preparing a paper about that and we are excited. On Mon, 2012-04-02 at 09:40 -0400, Louis Letourneau wrote: > That's very cool! > > "ask Ray to search for known things" > Where can I find more info on how to ask? > > If there's an explanation somewhere, just point me to it, I don't want > to waste your time explaining it to me :-) > > Thanks > 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 > >>> [email protected] > >>> 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 > >> [email protected] > >> 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 [email protected] https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
