• You can find a summary of all genomes in GenBank in this file.
• A similar file is also available for RefSeq genomes.

Parse the files to get "complete genomes" or any other criteria you are looking for.

use the 6th column to identify the taxonomy. Then to process ids by taxonomy use the taxonkit and csvtk

• taxonkit: https://github.com/shenwei356/taxonkit
• csvtk: https://github.com/shenwei356/csvtk
• publication: https://www.biorxiv.org/content/10.1101/513523v1

get the mammalian ids

taxonkit list --ids 40674 --indent "" | grep . > mammalian.ids.txt

filter the assembly file

wget https://ftp.ncbi.nlm.nih.gov/genomes/genbank/assembly_summary_genbank.txt
cat assembly_summary_genbank.txt | cut -f 1,6,8 | csvtk -t grep -f 2 -P  mammalian.ids.txt > mammalian.txt

this will give you 649 genomes, but not all are unique taxids

cat mammalian.txt | cut -f 2 | sort | uniq -c | sort -rn | wc -l

produces:

 297

If all you are after is a count (and not particularly interested in downloading the assemblies), you can do this from the NCBI Assembly web portal. This way, you won't have to bother downloading and installing a couple of other programs on your machine if you don't want to.

1. Search for the following in NCBI Assembly: mammals[Organism] AND latest_genbank[Properties]. This will return 633 assemblies. You can search for other broad categories such as 'rodents', 'plants', etc as well.

2. There may be multiple assemblies submitted for a single species. So, you need to flatten this list to a unique set of taxa. You can do this by following the link to Taxonomy page. On the right hand side of panel of the Assembly results page you will notice a 'Find related data' facet with a drop-down list of databases beneath it. From that drop-down list, choose 'Taxonomy' and click the 'Find items' button. You will be directed to a Taxonomy results page. The count there, 295, is what you are looking for.

I am not entirely sure why there is a discrepancy of 2, compared to the taxonkit/csvtk method described above; I did not download the two programs and run them on my own.