UPDATE 2020-11-21

If you have a list of NCBI assembly accessions with GCA or GCF prefixes, the easiest way to download data is to use the new tool NCBI Datasets. There is a web-interface to do this, if you don't want to bother with command line. If you do want to use the command line, you can use the datasets CLI tool as follows:

datasets download genome accession --inputfile assm_accs.txt --exclude-gff3 --exclude-protein --exclude-rna

where assm_accs.txt has NCBI assembly accessions, one per each line.

Note Currently, only the latest assembly accessions for a taxon are in the scope of NCBI Datasets. If you want to download older assemblies, you will have to use Entrez Direct as follows:

esearch -db assembly -query 'Bos taurus[organism] AND latest[filter]' \
    | esummary \
    | xtract -pattern DocumentSummary -element FtpPath_GenBank \
    | while read -r line ; 
    do
        fname=$(echo $line | grep -o 'GCA_.*' | sed 's/$/_genomic.fna.gz/') ;
        wget "$line/$fname" ;
    done

Here, I am first fetching the FTP path for the GenBank assembly using edirect tools and then use standard linux commands to download the genomic fasta file.

If your starting point is a file with a list of NCBI assembly accessions, you can wrap the command shown above in a bash loop like this:

cat assm_accs.txt | while read -r acc ; do
    esearch -db assembly -query $acc </dev/null \
        | esummary \
        | xtract -pattern DocumentSummary -element FtpPath_GenBank \
        | while read -r url ; do
            fname=$(echo $url | grep -o 'GCA_.*' | sed 's/$/_genomic.fna.gz/') ;
            wget "$url/$fname" ;
        done ;
    done