Bio-RetrieveAssemblies

Download WGS assemblies or annotation from GenBank. All accessions are screened against RefWeak.

Installation

cpanm Bio::RetrieveAssemblies

Usage

# 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