Last summer, I used refseq annotated genomes of different bivalves to build a species tree. Notebooks posts on that linked below.
This summer, I want to expand this tree to include selected bivalves (olys, cockles, others...) with genomes on NCBI even if they are not refseq annotated but am not sure how to tell if these genomes have been assembled similarly to the refseq ones or if they have similar coverage, thus I'm not sure whether or not they would be appropriate/comparable to include on my tree.
What are things to look for on a NCBI genome page to tell if an available has good coverage and/or is otherwise "high quality" -- are these things that even matter? What are other things I should be on the lookout for when selecting and comparing genomes? Eg-- Basket cockle (Clinocardium nuttallii) genome
prelim tree results
prelim tree methods
Last summer, I used refseq annotated genomes of different bivalves to build a species tree. Notebooks posts on that linked below.
This summer, I want to expand this tree to include selected bivalves (olys, cockles, others...) with genomes on NCBI even if they are not refseq annotated but am not sure how to tell if these genomes have been assembled similarly to the refseq ones or if they have similar coverage, thus I'm not sure whether or not they would be appropriate/comparable to include on my tree.
What are things to look for on a NCBI genome page to tell if an available has good coverage and/or is otherwise "high quality" -- are these things that even matter? What are other things I should be on the lookout for when selecting and comparing genomes? Eg-- Basket cockle (Clinocardium nuttallii) genome
prelim tree results
prelim tree methods