getKingdomAssemblySummary

database name. E.g. <code>refseq</code> or <code>genbank</code>.

Retrieval function of the assembly_summary.txt file 
from NCBI for all kingdoms.
The assembly_summary.txt files store available species on NCBI.

Perform metagenomic data retrieval and functional annotation
retrieval. In detail, this package aims to provide users with a standardized
way to automate genome, proteome, coding sequence ('CDS'), 'GFF', and metagenome
retrieval from 'NCBI' and 'ENSEMBL' databases. Furthermore, an interface to the 'BioMart' database
(Smedley et al. (2009) <doi:10.1186/1471-2164-10-22>) allows users to retrieve
functional annotation for genomic loci. Users can download entire databases such
as 'NCBI RefSeq' (Pruitt et al. (2007) <doi:10.1093/nar/gkl842>), 'NCBI nr',
'NCBI nt' and 'NCBI Genbank' (Benson et al. (2013) <doi:10.1093/nar/gks1195>) as
well as 'ENSEMBL' and 'ENSEMBLGENOMES' with only one command.

Hajk-Georg Drost

getKingdomAssemblySummary: Retrieve and summarise the assembly_summary.txt files from

Description

Usage

Arguments

See Also

Examples