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Old 06-08-2009, 03:05 AM   #1
vani s kulkarni
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Default velvet assembly

hi

Am using 'Velvet' assembly for my short read sequence from solexa.
I want to know about the parameters like hash length (K) and N50 in velvet in detail and in the manual these are not explained so good. And I saw the paper by Daniel R. zerbino and Ewan Birney but am not satisfied.

so any one can explain these parameters and how these are used in the decision of good assembly selection? or any web reference is also help full for me.

Thanks in advance....
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Old 06-09-2009, 10:07 AM   #2
bioinfosm
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Can you expand on specific questions?

The N50 length is the length-weighted median contig length. (50% of the nucleotides are situated on a contig longer than n50)
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Old 06-09-2009, 08:29 PM   #3
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You mean this http://www.ebi.ac.uk/~zerbino/velvet...th_choice.html
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Old 06-09-2009, 11:36 PM   #4
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Quote:
Originally Posted by bioinfosm View Post
Can you expand on specific questions?

The N50 length is the length-weighted median contig length. (50% of the nucleotides are situated on a contig longer than n50)
hi

how to select good assembly based on hash length and N50 in velvet denovo assembler?
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Old 06-09-2009, 11:40 PM   #5
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Quote:
Originally Posted by Melissa View Post
hi
thanks for the link

but I want to know how this hash length helps in selecting good assembly?
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Old 06-10-2009, 08:58 PM   #6
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Hash length is overlap b/w reads (based on this it makes graph).... if it more you get better assembly....if you keep less, there is a chance of mis-assemblies....I think maximum you can keep 31 (it should be odd number)
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Old 06-28-2009, 07:39 PM   #7
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Quote:
Originally Posted by Rao View Post
Hash length is overlap b/w reads ....I think maximum you can keep 31 (it should be odd number)
The latest version of Velvet now supports hash values (k) greater than 31. This could improve assemblies of longer reads.
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Old 06-28-2009, 08:44 PM   #8
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Thanks for the update...
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Old 06-30-2009, 06:43 AM   #9
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this plot might help. i generate one of these every time I do an assembly and pick a combination of parameters that keep me somewhere in the upper right of that plot. The exact choice depends on the purpose of the assembly.

the axes are in base pairs. the colored strata are cvCut cohorts. The points are kmers, increasing left to right (I have labeled one set for clarity)

increasing the kmer index will demand greater extension specificity and reduce the number of spurious contigs. If your sequencing went well and you have long reads (i.e. 1.5x-2x kmer) increasing the kmer should not be too detrimental to your total coverage (in this plot assembly length in base pairs). If your kmer is too high you will see a big dropoff in coverage without gaining N50.

increasing the cvCut will raise the contig depth threshold and also help discourage the formation of false contigs at the risk of missing areas of low coverage. If your cvCut is too low you will see a big hit to your N50 at all kmer lengths.
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Old 07-01-2009, 11:34 AM   #10
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@Zigster: that's awesome ... would you be willing to share your script for graphing? (R, I'd assume?)
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Old 07-01-2009, 11:36 AM   #11
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It's perl and R/Sweave glued together with a shell script

I'll try to get something usable up in googlecode soon
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Old 07-06-2009, 01:39 AM   #12
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hi
Thanks for your informations ,now I can try with different options...
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Old 08-24-2009, 03:02 PM   #13
Zigster
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as promised with better plots:

http://code.google.com/p/standardize...sembly-report/
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Old 08-24-2009, 03:39 PM   #14
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Looks great Just checked out the repository ^^ to look into the details

As a more basic R question, do you use ggplots2 to make the boxplots on the axis as on the first figure you posted here? I ran the testInstalledPackage function (tools library) and didn't see one like that.

Thanks
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Old 08-24-2009, 06:59 PM   #15
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that was done using scatterplot from the "car" package
ggplot is much more sophisticated, although I have yet to fully grasp the syntax
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Old 08-24-2009, 07:22 PM   #16
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Thanks! cor.plots and confidence.ellipse look interesting as well
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Old 08-24-2009, 11:42 PM   #17
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Hello,

this tool looks really handy IF you have your reference genome sequenced. For people working on plants, this is most often not the case. So I wonder why you use velvet, which is a de novo assembly tool, and not one of the reference based tools.

Do you have a solution for validating velvet results for people doing real de novo assembly?

Many thanks,
Steven

Last edited by strob; 08-24-2009 at 11:47 PM.
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Old 08-25-2009, 04:03 AM   #18
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i am doing de novo txome assembly of plants

basically I just use the closest related species to see if something unexpected is happening with the parameters
most of this short script is concerned with N50 and assembly size
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Old 08-26-2009, 01:33 AM   #19
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I would really like to test your tool, but it seems to use BLAT, which is for us as a company not freely available. Do you think you could incorporate another (complete free) alignment tool?
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Old 08-26-2009, 04:09 AM   #20
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Yes I will make the alignment part optional or BLAST-driven.
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