Description

A tool to quickly download assemblies from NCBI's Assembly database

Input

Name
Description
Pattern

meta (map)

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]

accessions (file)

List of accessions (one per line) to download

*.txt

taxids (file)

List of taxids (one per line) to download

*.txt

groups (string)

NCBI taxonomic groups to download. Can be a comma-separated list. Options are ['all', 'archaea', 'bacteria', 'fungi', 'invertebrate', 'metagenomes', 'plant', 'protozoa', 'vertebrate_mammalian', 'vertebrate_other', 'viral']

Output

Name
Description
Pattern

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Tools

ncbigenomedownload Documentation

Download genome files from the NCBI FTP server.

License: Apache Software License
Authors