Marina I am using Ray with paired end reads, but wondering if the defaults work for you? Something like:
mpiexec -np 64 ./Ray -k 25 -s Cleanup_454/sequences_.fastq -s Cleanup_ill/output_files/sequences_.fastq -o testK25def Regards, Ani --------------------------"The Answer Lies In The Genome"-------------------------- On Tue, Apr 5, 2016 at 3:36 PM, marina espigares <mesp...@uma.es> wrote: > El 05.04.2016 14:07, Animesh Sharma escribió: > >> Hi Marina, >> >> Which Ray version and how are you invoking it? If you simply assemble >> with -k and -input files, they won't call these other routines. >> >> Regards, >> >> Ani >> >> --------------------------"The Answer Lies In The >> Genome"-------------------------- >> >> On Tue, Apr 5, 2016 at 12:49 PM, marina espigares <mesp...@uma.es> >> wrote: >> >> Hello, >>> >>> I am using RAY to assembly the transcriptome of the chestnut tree. >>> It >>> can generate the contigs pretty fast but the program keep working on >>> the >>> BiologicalAbundances for a long time. What are those files for? It >>> that >>> affects the assembly results?, it is possible to deactivate? >>> >>> Thank you >>> >>> -- >>> Marina Espigares >>> >>> >>> >> ------------------------------------------------------------------------------ >> >>> _______________________________________________ >>> Denovoassembler-users mailing list >>> Denovoassembler-users@lists.sourceforge.net >>> https://lists.sourceforge.net/lists/listinfo/denovoassembler-users >>> [1] >>> >> >> >> >> Links: >> ------ >> [1] https://lists.sourceforge.net/lists/listinfo/denovoassembler-users >> > > Hello Ani, > > I'm using ray/2.3.1, and I call it this way: > > -mpiexec -np 64 Ray -k 25 -s Cleanup_454/sequences_.fastq -s > Cleanup_ill/output_files/sequences_.fastq -route-messages -connection-type > debruijn -routing-graph-degree 4 > > > Any suggestion? > > Regards > > Marina >
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