>From your LibraryStatistics.txt: AverageOuterDistance: 93
But it is supposed to be 200. This is strange. You can provide the average manually to Ray with this: mpiexec -n 78 Ray -k 41 -o test41 \ -p file_1.fastq.bz2 file_2.fastq.bz2 200 20 Otherwise, the detected distance of 93 may be the problem. On 26/09/12 01:43 PM, Adam Caldwell wrote: > FR, and around 200 (Id have to double check though). > > On Wed, Sep 26, 2012 at 3:40 AM, Sébastien Boisvert > <sebastien.boisver...@ulaval.ca> wrote: >> Hello, >> >> What is the strand orientation of your fosmid data ? >> >> And what is the expected insert size (including both read lengths and >> gap) ? >> >> On 25/09/12 07:07 PM, Adam Caldwell wrote: >>> On Mon, Sep 24, 2012 at 12:44 PM, Sébastien Boisvert >>> <sebastien.boisver...@ulaval.ca> wrote: >>>> Hello, >>>> >>>> On 24/09/12 03:30 PM, Adam Caldwell wrote: >>>>> On Mon, Sep 24, 2012 at 5:47 AM, Sébastien Boisvert >>>>> <sebastien.boisver...@ulaval.ca> wrote: >>>>>> Hello, >>>>>> >>>>>> On 22/09/12 01:28 AM, Adam Caldwell wrote: >>>>>>> Is there any documentation for the metagenomic assembly abilities of >>>>>>> Ray? I couldnt find any. >>>>>> >>>>>> We have a paper that we need to resend in revised form about Ray Méta >>>>>> (de novo >>>>>> metagenome assembly) and Ray Communities (biological abundances and >>>>>> taxonomic profiling). >>>>>> >>>>>>> The reason I ask is it performs surprisingly >>>>>>> poorly on my data. >>>>>> >>>>>> What type of data exactly ? >>>>> >>>>> These are pools of several hundred fosmids (~40kb pieces), sequenced >>>>> with Illumina. They are 2x75bp, paired end. While this is similar to a >>>>> metagenomic project in that there are hundreds on different species >>>>> sequenced together, each clone should have roughly equal coverage. I >>>>> have good assemblies with Velvet/MetaVelvet and ABySS, so it is >>>>> curious that Ray doesnt come close, when it works so well for single >>>>> genomes. >>>>> >>>> >>>> What k-mer length are you using ? >>>> >>>> Does Ray detect paired information correctly for your input data >>>> (look in LibraryStatistics.txt) >>> >>> I tried 31 and 41, with 41 giving slightly better results. Paired >>> reads seem to be detected: >>> >>> NumberOfPairedLibraries: 1 >>> >>> LibraryNumber: 0 >>> InputFormat: TwoFiles,Paired >>> DetectionType: Automatic >>> File: reads_archive/lane1a_reads/lane1a_novec_paired.1.fastq >>> NumberOfSequences: 7595472 >>> File: reads_archive/lane1a_reads/lane1a_novec_paired.2.fastq >>> NumberOfSequences: 7595472 >>> Distribution: lane1a_ray41/Library0.txt >>> Peak 0 >>> AverageOuterDistance: 93 >>> StandardDeviation: 33 >>> >>>> >>>>> I take it from your response, there is no specific flag to enable a >>>>> metagenomic mode? Does Ray somehow detect whether a sample is single >>>>> or metagenome, or has the algorithm just been tuned to handle both >>>>> types equally well? >>>>> >>>> >>>> Indeed, the new code handles both single-genome multiple-cell assembly and >>>> multiple-genome multiple-cell assemblies. >>>> >>>> It is a generalization, if you will. >>> >>> Seems there isnt much I can do, then. Not really a worry, I was just >>> trying to evaluate an assortment of assemblers for this project, and >>> it seems others are better suited. >>> >>>> >>>>>> >>>>>>> Multiple other assemblers had a N50 an order of >>>>>>> magnitude higher, and largest contigs over twice as long. >>>>>>> >>>>>>> I am assuming I am missing something, or perhaps its not completely >>>>>>> implemented? 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