Using assembly_summary_refseq.txt from
ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/assembly_summary_refseq.txt
I coppied the second row (contains the titles for the table):
sed '2!d' assembly_summary_refseq.txt > BfragRefseqAssemblies.txt
I grepped all the Bacteroides fragilis, by running:
grep 'Bacteroides fragilis' assembly_summary_refseq.txt >> BfragRefseqAssemblies.txt
There were 107 results. To create a list of ftp addresses for download I used:
cut -f 20 BfragRefseqAssemblies.txt > BfragRefseqAssembliesFTP.txt
I then used:
for file in `cat BfragRefseqAssembliesFTP.txt`;do wget --recursive --no-host-directories --cut-dirs=2 $file/; done
After downloading all genomes I went throught the Pan-genome workflow.