Fast download BLAST databases from NCBI

Database files (volumes) are downloaded in parallel: number of threads to use is determined automatically. MD5 checksum is verified and the database volume extracted upon download. Database volumes are not downloaded in a particular order. The volumes are updated if a newer version is available on the server, or re-downloaded if corrupt. Aborted downloads are safely resumed.

ncbi-blast-dbs is faster than NCBI's update_blastdb.pl. But unlike update_blastdb.pl, which is a pure Perl script, ncbi-blast-dbs delegates download and checksum verification to wget and md5sum and is thus not as universal.

Installation

gem install ncbi-blast-dbs

Usage

List available BLAST databases

ncbi-blast-dbs

Download all volumes of a BLAST database

ncbi-blast-dbs nt nr

Databases are downloaded one after the other while volumes of each database are downloaded in parallel.

ncbi-blast-dbs nt nr

NCBI expects users to submit their email address when downloading data from their FTP server. To comply with that, download as:

email="my email address here" ncbi-blast-dbs nr