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-   -   Is this assembly reasonable? (http://seqanswers.com/forums/showthread.php?t=30754)

lkral 06-02-2013 03:53 PM

Is this assembly reasonable?
 
I have completed some de novo assemblies of MiSeq generated 250PE reads with Minia and SSPACE. I've posted a description of the outcomes and some quality checks at the following site:

http://www.dartergenomics.org/tallapoosa-darter-genome

For those of you with experience in assemblies, could you please look this over and let me know if the scaffold distributions I ended up with are reasonable given the MiSeq data?

Thanks.

rchikhi 06-03-2013 01:55 PM

As an author of Minia, I would say that it looks good, but I would be a bit biased :) Thanks for using the software.

The k=73 min_abundance=2 assembly appears to be better than the k=63 min_abundance=3, consistently over all metrics. Thus you could focus on the k=73 one.

I have not tested them, but two tools can help you further evaluate accuracy metrics of an assembly without a reference:
https://github.com/vezzi/FRC_align
http://www.sanger.ac.uk/resources/software/reapr/

Also you mentioned that there are ~53M paired reads, yielding 13x coverage. Does each of the 53M paired reads consist of two mates of length 250bp? if so the coverage should be multiplied by two.

lkral 06-04-2013 04:56 AM

Thanks for the references.

And to be clear, there are 53 million individual reads.


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