Ran dipSpades for a diploid fungus genome -- now what?
Entering edit mode
5.3 years ago
Lina F ▴ 200

Hi all,

I successfully ran dipSpades for a diploid fungus genome but now I am feeling stuck on how to analyze the resulting output.

I got the following results:

consensus_contigs.fasta -> 300 contigs
paired_consensus_contigs.fasta -> 216 contigs
unpaired_consensus_contigs.fasta -> 84 contigs

Do you have any advice for how to continue with the analysis beyond running dipspades?

Specifically, I am wondering where or the how the phasing information is stored.

For example, on the manual's website, it states "paired_consensus_contigs.fasta - file in FASTA format with a subset of consensus contigs that have a polymorphism detected on them".

So if I compare the contigs from consensus_contigs.fasta and paired_consensus_contigs.fasta that have the name, does that provide me with SNP information?

Thanks for any suggestions!

diploid genome assembly dipspades • 1.5k views
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Is the genome diploid highly polymorphic which is what dipSpades is specifically designed for? What are you exactly hoping to get from this genome?

Entering edit mode

Yes, my lab folks tell me it is considered to be a highly polymorphic diploid given dipSpades's definition ("haplomes that differ from each other by 0.4–10%".).

Ultimately, I'm trying to get a somewhat reliable reference with phasing information. The final assembly should be about 16 megabases. I currently have the following number of bases:

consensus_contigs.fasta -> 8,917,627 bases
paired_consensus_contigs.fasta -> 8,389,861 bases
unpaired_consensus_contigs.fasta -> 527,766 bases
Entering edit mode

Hi OP,

Did you ever figure out what was best to do? I feel stuck after doing genome annotation with MAKER. I used the consensus_contigs.fasta file for downstream analysis, but I am not sure if this is the right file to have proceeded with. I feel like there are a lot of duplicated genes reported from MAKER, which I don't want to skew my results.

Thanks, Morgan

Entering edit mode

Unfortunately, I couldn't figure out what the best thing to do was. None of the advice I found on the internet made me feel confident in dipSpades :-(


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