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? Im using Ray cloned from git today. >>>>> >>>>> ------------------------------------------------------------------------------ >>>>> How fast is your code? >>>>> 3 out of 4 devs don\\\'t know how their code performs in production. >>>>> Find out how slow your code is with AppDynamics Lite. >>>>> http://ad.doubleclick.net/clk;262219672;13503038;z? >>>>> http://info.appdynamics.com/FreeJavaPerformanceDownload.html >>>>> _______________________________________________ >>>>> Denovoassembler-users mailing list >>>>> Denovoassembler-users@lists.sourceforge.net >>>>> https://lists.sourceforge.net/lists/listinfo/denovoassembler-users >>>> >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> Live Security Virtual Conference >>>> Exclusive live event will cover all the ways today's security and >>>> threat landscape has changed and how IT managers can respond. Discussions >>>> will include endpoint security, mobile security and the latest in malware >>>> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >>>> _______________________________________________ >>>> Denovoassembler-users mailing list >>>> Denovoassembler-users@lists.sourceforge.net >>>> https://lists.sourceforge.net/lists/listinfo/denovoassembler-users >> ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Denovoassembler-users mailing list Denovoassembler-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
