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!