This is a quick introduction to using NCBI's Datasets resource within the Galaxy project.
Whether at NCBI or in Galaxy, Datasets allows you to download sequences and metadata for
genomes, transcripts and proteins, either in a browser, or from the command line.
Datasets currently provides access to more than 24,000 eukaryotic genomes,
one point two million bacteria, 10,000 archaea,
and 50,000 viruses.
Let's see how you can access all of these genomes within Galaxy.
This is the public server page for Galaxy, usegalaxy.org.
It’s advantageous to have an account so that you can save workflows and results, and
access them from anywhere.
On the server page, you see three panels: on the left there’s a list of available
tools. On the right is the History panel. In this
case, we are starting with an empty history.
And the center panel is where you interact with the tools and data.
Let's find the NCBI Datasets tool. You could, of course, search for the name NCBI datasets,
or find it under Get Data.
When you click on NCBI Datasets Genomes, the tool appears in central panel.
The default option is to download genomes by accession, but you can choose the taxon
option instead, which accepts virtually any taxon level. We'll
be downloading data for the Ugandan red colobus, Piliocolobus tephrosceles, is just a bit.
The “Filters and Limit” menu let's you choose the source of the assemblies, so you
can limit to Reference genomes, for example, or only genomes with annotation.
And the “File Choices” menu allows you to customize the data package to get only
the file types you want.
I'll get the default package by clicking the Execute button.
The central panel shows that the job was submitted successfully. And on the right we see the
files that are being downloaded.
The gray color indicates that the jobs are queued.
Once they start running, the color changes to orange.
And if the jobs are successful, the color changes to green.
In Galaxy, files are organized by type. We have two metadata reports in JSON format;
a data report, which includes metadata for all genomes downloaded, and then one sequence
data report per assembly.
We have the FASTA sequences, and an annotation report in GFF3 format.
We downloaded only one genome, but if we had requested multiple genome assemblies, each
file would be identified by the assembly accession number.
Let’s take a closer look at the genomic cds fasta file.
By the way, this is the Assembly accession number for our genome.
Note that you can download these files for local workflows, or perform your analyses
within Galaxy.
And there are several Galaxy tools that benefit from a reference genome retrieved with NCBI
Datasets.
Under Genomic Analysis you have Annotation tools such as Maker;
Mapping tools, such as minimap2 and BWA-MEM2; And RNA-seq tools like StringTie, for transcript
assembly.
That's our quick introduction. Galaxy offers many Help options,
as does Datasets, and you can provide feedback, and ask us questions
by using the Feedback button, or writing to,
info@ncbi.nlm.nih.gov
NCBI Datasets is part of the NIH Comparative Genomics Resource (CGR), which is an NLM project
to facilitate comparative genomics analyses for all eukaryotic organisms.