>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? Im using Ray cloned from git today.
>>>>>>>
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