How to manually download the metadata of all the available genomes of an organism in NCBI

How to manually download the metadata of all the available genomes of an organism in NCBI?

AUTHOR: Dr Asad Prodhan https://asadprodhan.github.io/

Step 1: Search your organism in the NCBI database

• Go to the NCBI website: https://www.ncbi.nlm.nih.gov/

• Search your organism as shown for Fusarium in the red rectangular box in Fig. 1

• The search results will be displayed under different categories (Fig. 1)

• Click on the Genomes database as indicated by the red hexagon in Fig. 1

Figure 1: Search your organism in the NCBI database.

Step 2: Select the metadata of your interest

• You will see something like Fig. 2

• Tick the assembly box as indicated by the red circle in the Fig. 2

• Click on the Select columns tab as indicated by the red rectangle in the Fig. 2

Figure 2: Select the metadata of your interest.

• Select the metadata of your interest and apply (Fig. 3)

Figure 3: Available metadata.

Step 3: Download the metadata

• Click on the Download tab as indicated by the red circle in Fig. 4

• Select Download Table from the drop-down menu

• Select Tab-separated values (TSV) format

• Click Download

Figure 4: Download the metadata.

Step 3: Convert the TSV file into excel sheet

• A TSV file containing the metadata will be downloaded.

• You can open the TSV file in excel like Fig. 5.

Figure 5: Metadata sheet.

Now, you have an excel sheet containing the metadata of all the available genome sequences of Fusarium.

You can sort out these information and short list the assembly numbers that you want download.

See this tutorial on how to download genome sequences automatically:

https://github.com/asadprodhan/How-to-download-all-the-available-genome-sequences-of-an-organism-automatically