Is this assembly reasonable?

lkral · 06-02-2013, 03:53 PM

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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06-02-2013, 03:53 PM	#1
lkral Member Location: Carrollton, GA Join Date: May 2011 Posts: 27	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.

06-03-2013, 01:55 PM	#2
rchikhi Member Location: France Join Date: Jan 2013 Posts: 13	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.

06-04-2013, 04:56 AM	#3
lkral Member Location: Carrollton, GA Join Date: May 2011 Posts: 27	Thanks for the references. And to be clear, there are 53 million individual reads.