Download WGS assemblies or annotation from GenBank. All accessions are screened against RefWeak.
cpanm Bio::RetrieveAssemblies
# Download all assemblies for Salmonella
retrieve_assemblies Salmonella
# Download all assemblies for Typhi
retrieve_assemblies Typhi
# Download all assemblies in a BioProject
retrieve_assemblies PRJEB8877
# Set the output directory
retrieve_assemblies -o my_salmonella Salmonella
# Get GFF3 files instead of GenBank files
retrieve_assemblies -f gff Salmonella
# Get annotated GFF3 files instead of GenBank files (compatible with Roary)
retrieve_assemblies -a -f gff Salmonella
# Get FASTA files instead of GenBank files
retrieve_assemblies -f fasta Salmonella
# Search for a different category, VRT/INV/PLN/MAM/PRI/ENV (default is BCT)
retrieve_assemblies -p MAM Canis
# This message
retrieve_assemblies -h