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.