ask for idea about de novo genome

[camelbbs]

Recently we sequenced an uncommon animal genome. I want to ask what can we do to that?
Call SNP/Indel? seems can't, because there is no reference.

compare with other species? or do comparative genomics.

Anyone have good idea?

[adaptivegenome]

What animal is it? And what motivated you guys to sequence it?

Recently we sequenced an uncommon animal genome. I want to ask what can we do to that?
Call SNP/Indel? seems can't, because there is no reference.

compare with other species? or do comparative genomics.

Anyone have good idea?

[camelbbs]

It's a kind of fish. So it's useless?

[adaptivegenome]

It's a kind of fish. So it's useless?

I am curious why you guys sequenced it if you don't know what to do with it; however I am not saying that it is useless. You might (if the reads are long enough and coverage is good enough) assemble the sequence and compare to similar fish genomes, but without knowing more about the fish and the motivation for the project its hard to give you any advice.

[krobison]

Even without a reference, you should be able to call SNPs and other variants -- you make your reference by de novo assembly & then call. Of course, you may overcall some variants that are really due to duplications, but still some useful information could be extracted.

Did you have end-of-year budget to burn off or something? Does seem odd to sequence first and design the experiments after the fact.

[camelbbs]

Even without a reference, you should be able to call SNPs and other variants -- you make your reference by de novo assembly & then call. Of course, you may overcall some variants that are really due to duplications, but still some useful information could be extracted.

Did you have end-of-year budget to burn off or something? Does seem odd to sequence first and design the experiments after the fact.

Because we do PCR, race, etc to get the gene of that fish we want, tired of experiment with very limited info, we sequenced that fish and hope it can help improve the experiment. But now for the whole genome sequencing, we think it must have some better info we can get in large-scale analysis than separate bench work.
Thanks anyway.
The question: if we use the genome self as a reference, if like that, how to call variants, as they are the same things.

[Zam]

There is a (our) published tool precisely for detecting variants from sequence data without using a reference, you could try that:

Z Iqbal*, M Caccamo*, I Turner, P Flicek, G McVean.
De novo assembly and genotyping of variants using colored de Bruijn graphs.
Nat Genet. 2012 Jan 8;44(2):226-32. doi: 10.1038/ng.1028.

http://cortexassembler.sourceforge.net/index_cortex_var.html

Just give it the reads, and it will assemble variants. You can email me directly (zam AT well.ox.ac.uk) if you want more information, or check out the Google group (there is a link on the page I give above). It's important to be clear on what your goals are though.

best

Zam

[camelbbs]

I am curious why you guys sequenced it if you don't know what to do with it; however I am not saying that it is useless. You might (if the reads are long enough and coverage is good enough) assemble the sequence and compare to similar fish genomes, but without knowing more about the fish and the motivation for the project its hard to give you any advice.

do you have an idea about compare the two genomes? BLAST? Thanks!

[Zam]

Again - Cortex will do it
cheers
Zam

[camelbbs]

Again - Cortex will do it
cheers
Zam

Well..I'll try it. Thanks a lot!