A one-stop shop for finding, browsing, and downloading genomic data.

References:

• O'Leary NA, Cox E, et al. Exploring and retrieving sequence and metadata for species across the tree of life with NCBI Datasets Sci Data. 2024 Jul 5;11(1):732.

• NCBI Datasets Main Site

Running NCBI Datasets is not allowed on the Biowulf login node. Please submit a batch job, or allocate an interactive node.

• Module Name: ncbi-datasets (see the modules page for more information)

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 12345678
salloc.exe: job 12345678 queued and waiting for resources
salloc.exe: job 12345678 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load ncbi-datasets

[user@cn3144 ~]$ datasets summary gene gene-id 1 2 3 9 10 11 12 13 14 15 16

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 12345679
[user@biowulf ~]$

Create a batch input file (e.g. sbatch.sh). For example:

#!/bin/bash
set -e
module load ncbi-datasets
datasets summary gene symbol ACRV1 A2M --taxon human

Submit this job using the Slurm sbatch command.

sbatch sbatch.sh