Missing plants in PlusPFP

[bioreactordan]

Hi,

I'm using PlusPFP to identify algae species (plants). However, the algae species of interest (Chlorella sorokiniana) is not represented in the index even though it is listed in RefSeq with a full genome as of October 2022. Did you filter RefSeq for plants in any way that would remove certain genomes? I cross-checked RefSeq plant with the .txt file and some of the 2,663 organisms listed under the plant category in RefSeq are not in the index.

Thanks

[mclaugsf]

We noticed the same thing; Humulus lupulus (hops) is missing along with anything from the Humulus genome. Curious how this got skipped while Cannabis sativa is present?

[BenLangmead]

I can unravel at least 1 level of the mystery, which is that we use this file to determine what to download: https://ftp.ncbi.nlm.nih.gov/genomes/refseq/plant/assembly_summary.txt

And the mentioned genome seems not to be in that file.