getMetaGenomeSummary

Retrieval function of the assembly_summary.txt file 
from NCBI genbank metagenomes.
This files stores all available metagenome projects on NCBI Genbank.

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

getMetaGenomeSummary: Retrieve the assembly_summary.txt file from NCBI genbank metagenomes

Description

Usage

Arguments

See Also

Examples