How to Download All Bacterial Genomes from NCBI
If you are interested in studying the diversity and evolution of bacteria, you might want to download all bacterial genomes available in public databases. This can be useful for comparative genomics, phylogenetics, metagenomics, and other applications. In this article, we will show you how to download all bacterial genomes from the National Center for Biotechnology Information (NCBI), one of the largest and most comprehensive repositories of biological data in the world.
Introduction
What are bacterial genomes and why download them?
Bacteria are microscopic organisms that belong to the domain of prokaryotes, which are the earliest forms of life on Earth. Bacteria have diverse shapes, sizes, habitats, and metabolic capabilities. They can cause diseases, but they can also be beneficial for humans and other living beings. For example, bacteria are involved in fermentation, biodegradation, nitrogen fixation, symbiosis, and biotechnology.
download all bacterial genomes ncbi
The genome of a bacterium is the complete set of genetic information encoded in its DNA. Most bacteria have a single circular chromosome that contains all the essential genes for survival and reproduction. Some bacteria also have extra-chromosomal elements called plasmids that carry accessory genes that can confer advantages such as antibiotic resistance or virulence factors.
By downloading all bacterial genomes, you can access a wealth of information about the diversity and evolution of these fascinating organisms. You can compare different strains or species of bacteria, identify genes or regions of interest, reconstruct phylogenetic trees, analyze gene expression or regulation, and more.
What is NCBI and what resources does it offer?
The National Center for Biotechnology Information (NCBI) is a branch of the U.S. National Institutes of Health (NIH) that provides free access to a variety of biological databases, tools, and services. NCBI hosts millions of records of nucleotide sequences, protein sequences, structures, genomes, genes, publications, and more. You can search, browse, analyze, and download data from NCBI using its web interface or its application programming interface (API).
One of the main resources that NCBI offers is the Genome database, which organizes information on genomes from all domains of life, including sequences, maps, chromosomes, assemblies, and annotations. You can find genome data for thousands of bacterial species and strains in NCBI Genome. You can also use other NCBI resources such as Assembly, BioProject, BioSample, GenBank, RefSeq, BLAST, and Datasets to access and analyze genome data.
Methods
Using the NCBI FTP site
One way to download all bacterial genomes from NCBI is to use its File Transfer Protocol (FTP) site. FTP is a standard network protocol that allows users to transfer files between computers over the Internet. The NCBI FTP site contains directories and files for various NCBI databases and resources. You can access the FTP site using a web browser or an FTP client software.
Finding the bacterial genomes directory
To find the directory that contains all bacterial genomes in NCBI FTP site, you need to follow these steps:
Go to , which is the root directory of the FTP site.
Navigate to , which is the directory for genome data.
Navigate to , which is the directory for all genome assemblies.
Navigate to , which is the directory for RefSeq genome assemblies. RefSeq is a curated collection of high-quality genome sequences and annotations from NCBI.
Navigate to , which is the first subdirectory of RefSeq genome assemblies.
Look for the subdirectories that start with is the directory for Escherichia coli strain K-12 MG1655.
Repeat steps 4 to 6 for the other subdirectories of RefSeq genome assemblies, such as , and so on, until you find all the bacterial genomes you want to download.
Choosing the assembly level and format
Once you find the directory for a bacterial genome, you need to choose the assembly level and format of the data you want to download. The assembly level refers to the degree of completeness and contiguity of the genome sequence. There are four assembly levels in NCBI:
Complete Genome: The entire genome sequence is represented in a single, gapless, and circular sequence.
Chromosome: The genome sequence is represented in one or more sequences that correspond to the chromosomes of the organism.
Scaffold: The genome sequence is represented in one or more sequences that are composed of ordered and oriented contigs (continuous segments of DNA).
Contig: The genome sequence is represented in one or more sequences that are not ordered or oriented.
The format refers to the file type and structure of the data. There are several formats available in NCBI, such as FASTA, GenBank, GFF, and WGS. The most common formats are:
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FASTA: A plain text format that contains only the nucleotide sequence of the genome, without any annotation or metadata.
GenBank: A plain text format that contains both the nucleotide sequence and the annotation of the genome, as well as metadata such as accession number, version, source, and references.
GFF: A plain text format that contains only the annotation of the genome, without the nucleotide sequence. It consists of nine tab-delimited columns that describe the features and attributes of each genomic region.
WGS: A compressed binary format that contains both the nucleotide sequence and the annotation of the genome, as well as metadata. It is optimized for large-scale sequencing projects and can be accessed using specialized tools such as NCBI SRA Toolkit or NCBI Datasets.
To choose the assembly level and format of the data you want to download, you need to follow these steps:
Go to the directory for a bacterial genome that you found in the previous step.
Look for the files that have the extension .fna, .gbff, .gff, or .wgs. These are the files that contain genome data in FASTA, GenBank, GFF, or WGS format, respectively.
Look at the file name and identify the assembly level by the prefix. The prefix can be one of these four options:
NC_: Complete Genome
NZ_: Chromosome
NW_: Scaffold
NZ_: Contig
Select the file that matches your preferred assembly level and format. For example, if you want to download a complete genome in GenBank format, look for a file that has the prefix NC_ and the extension .gbff.
Repeat steps 1 to 4 for each bacterial genome that you want to download.
Downloading the data using an FTP client
To download the data using an FTP client, you need to follow these steps:
Install an FTP client software on your computer. There are many free and open-source FTP clients available online, such as FileZilla, WinSCP, Cyberduck, or FireFTP.
Open your FTP client and connect to as the host name, anonymous as the user name, and your email address as the password.
Navigate to the directory and file that you want to download using the FTP client interface. You can use the same steps as described in the previous sections to find the bacterial genomes directory, choose the assembly level and format, and select the file.
Drag and drop the file from the FTP site to your local computer or use the download option in your FTP client.
Wait for the download to complete. The download time may vary depending on the size of the file and your Internet connection speed.
Repeat steps 3 to 5 for each file that you want to download.
Using the NCBI Datasets tool
Another way to download all bacterial genomes from NCBI is to use the Datasets tool. Datasets is a new NCBI service that allows users to easily access and download biological data in a standardized and convenient way. You can use Datasets to search, browse, filter, and download data from various NCBI databases, such as Genome, Gene, Protein, SRA, and PubChem. You can use Datasets through its web interface or its command-line tool.
Installing the Datasets command-line tool
To install the Datasets command-line tool, you need to follow these steps:
Go to , which is the official documentation page for the Datasets command-line tool.
Choose your operating system (Windows, Mac, or Linux) and follow the instructions to download and install the tool on your computer.
Open a terminal or command prompt window and type datasets --version to verify that the tool is installed correctly. You should see a message that shows the version number of the tool.
Searching for bacterial genomes by taxonomic name or accession
To search for bacterial genomes by taxonomic name or accession using the Datasets command-line tool, you need to follow these steps:
Open a terminal or command prompt window and type datasets summary genome taxon bacteria to get a summary of all bacterial genomes available in NCBI. You should see a table that shows the number of genomes, assemblies, chromosomes, plasmids, organelles, and sequences for each bacterial taxonomic group.
Type datasets summary genome taxon "taxonomic name" to get a summary of bacterial genomes for a specific taxonomic name. For example, type datasets summary genome taxon "Escherichia coli" to get a summary of E. coli genomes. You can use any valid taxonomic name or rank, such as species, genus, family, order, class, phylum, or domain.
Type datasets summary genome accession "accession number" to get a summary of a bacterial genome for a specific accession number. For example, type datasets summary genome accession GCF_000005845.2 to get a summary of E. coli strain K-12 MG1655 genome. You can use any valid accession number for a genome assembly or sequence in NCBI.
Type datasets list genome taxon "taxonomic name" or datasets list genome accession "accession number" to get a list of all bacterial genomes for a specific taxonomic name or accession number. For example, type datasets list genome taxon "Escherichia coli" or datasets list genome accession GCF_000005845.2. You should see a table that shows the accession number, version, assembly name, bioproject id, biosample id, and organism name for each genome.
Type --help after any command to get more information and options for that command.
Downloading the data package using the Datasets tool
To download the data package using the Datasets tool, you need to follow these steps:
Type datasets download genome taxon "taxonomic name" or datasets download genome accession "accession number" to download all bacterial genomes for a specific taxonomic name or accession number. For example, type datasets download genome taxon "Escherichia coli" or datasets download genome accession GCF_000005845.2. You should see a message that shows the progress and status of the download. The download time may vary depending on the number and size of the genomes and your Internet connection speed.
Wait for the download to complete. The downloaded data will be saved as a zip file in your current working directory. The zip file will have a name that starts with ncbi_dataset and ends with the date and time of the download.
Unzip the zip file to extract the data package. The data package will contain a directory named ncbi_dataset that has several subdirectories and files. The subdirectories and files will vary depending on the type and number of genomes you downloaded, but they will typically include:
data/: A directory that contains the genome data files in various formats, such as FASTA, GenBank, GFF, WGS, and JSON.
data_report.jsonl: A file that contains a summary of the genome data in JSON format.
dataset_catalog.json: A file that contains metadata about the data package in JSON format.
README.md: A file that contains instructions and information about the data package in Markdown format.
Repeat steps 1 to 4 for each taxonomic name or accession number that you want to download.
Conclusion
Summary of the main points
In this article, we have shown you how to download all bacterial genomes from NCBI using two methods: using the NCBI FTP site or using the NCBI Datasets tool. Both methods have advantages and disadvantages, depending on your preferences and needs. Here are some key points to remember:
The NCBI FTP site allows you to access and download data from various NCBI databases and resources, including Genome, Assembly, BioProject, BioSample, GenBank, RefSeq, BLAST, and Datasets.
The NCBI FTP site requires you to use an FTP client software or a web browser to connect to the FTP site and navigate to the directory and file that you want to download.
The NCBI FTP site allows you to choose the assembly level and format of the genome data, such as Complete Genome, Chromosome, Scaffold, Contig, FASTA, GenBank, GFF, or WGS.
The NCBI Datasets tool allows you to easily access and download data from various NCBI databases in a standardized and convenient way, such as Genome, Gene, Protein, SRA, and PubChem.
The NCBI Datasets tool requires you to install the Datasets command-line tool on your computer and use it to search for bacterial genomes by taxonomic name or accession number.
The NCBI Datasets tool downloads the genome data as a zip file that contains a data package with several subdirectories and files in various formats.
Recommendations and tips
Here are some recommendations and tips for downloading all bacterial genomes from NCBI:
Before downloading all bacterial genomes, make sure you have enough disk space and Internet bandwidth to store and transfer the data. The size of the data can vary depending on the number and complexity of the genomes, but it can be several gigabytes or more.
After downloading all bacterial genomes, make sure you check the integrity and quality of the data. You can use tools such as md5sum or sha256sum to verify the checksums of the files. You can also use tools such as FASTQC or QUAST to assess the quality of the sequences and assemblies.
If you encounter any problems or errors while downloading all bacterial genomes from NCBI, you can contact NCBI for support or feedback. You can use their online form at .
Frequently Asked Questions
What are some applications of downloading all bacterial genomes from NCBI?
Some applications of downloading all bacterial genomes from NCBI are:
Comparative genomics: You can compare different strains or species of bacteria to identify similarities and differences in their genome structure, content, function, and evolution.
Phylogenetics: You can reconstruct the evolutionary history and relationships of bacteria based on their genome sequences and annotations.
Metagenomics: You can analyze the diversity and function of bacterial communities in different environments or samples based on their genome sequences and annotations.
Gene expression or regulation: You can study how bacteria express or regulate their genes in response to different conditions or stimuli based on their genome sequences and annotations.
Biotechnology: You can discover or engineer new enzymes, pathways, products, or applications from bacteria based on their genome sequences and annotations.
How can I download all bacterial genomes from NCBI in a single file?
If you want to download all bacterial genomes from NCBI in a single file, you can use the NCBI Datasets tool with the --all option. This option will download all the genomes that match your query as a single zip file. For example, you can type datasets download genome taxon bacteria --all to download all bacterial genomes in a single file. However, be aware that this option may take a long time and a lot of disk space to complete.
How can I filter or refine my search for bacterial genomes in NCBI?
If you want to filter or refine your search for bacterial genomes in NCBI, you can use the NCBI Datasets tool with the --filter option. This option will allow you to specify criteria such as assembly level, assembly source, assembly status, release type, or annotation release date. For example, you can type datasets download genome taxon bacteria --filter "assembly_level=complete" to download only complete bacterial genomes. You can also use the --exclude-genbank or --exclude-refseq options to exclude GenBank or RefSeq genomes from your download.
How can I update my downloaded bacterial genomes from NCBI?
If you want to update your downloaded bacterial genomes from NCBI, you can use the NCBI Datasets tool with the --updated-since option. This option will allow you to specify a date and download only the genomes that have been updated since that date. For example, you can type datasets download genome taxon bacteria --updated-since 2023-01-01 to download only the bacterial genomes that have been updated since January 1, 2023. You can also use the --dry-run option to preview the list of genomes that will be downloaded without actually downloading them.
How can I access and analyze my downloaded bacterial genomes from NCBI?
If you want to access and analyze your downloaded bacterial genomes from NCBI, you can use various tools and software depending on your needs and preferences. Some examples are:
NCBI SRA Toolkit: A software suite that allows you to access and manipulate data in WGS format.
NCBI BLAST: A software suite that allows you to compare your sequences with other sequences in NCBI databases.
Mauve: A software suite that allows you to align and visualize multiple bacterial genomes.
Mega: A software suite that allows you to perform phylogenetic analysis of bacterial genomes.
R: A programming language and environment that allows you to perform statistical analysis and visualization of bacterial genomes.
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