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Lautaro Torres
Lautaro Torres

Download bacterial genome sequences from the International Nucleotide Sequence Database Collaboration


How to Download Bacterial Genome Data from NCBI




Bacterial genomes are the complete sets of genetic information of bacteria. They contain the instructions for how bacteria look and function, both externally and internally. Bacterial genomes are encoded in DNA molecules that are organized into genes, which are units of biological information. Studying bacterial genomes can help us understand the diversity, evolution, ecology, and pathogenicity of bacteria.


One of the best sources of bacterial genome data is the National Center for Biotechnology Information (NCBI), which is a part of the U.S. National Library of Medicine. NCBI provides access to a wealth of biological information, including genome sequences, annotations, alignments, phylogenies, and more. NCBI also provides tools and services for searching, analyzing, and downloading biological data.




download bacterial genome



Downloading bacterial genome data from NCBI can have many benefits for researchers, educators, students, and enthusiasts. You can use the downloaded data for offline analysis, comparison, visualization, education, or personal interest. You can also use the downloaded data to create your own databases, pipelines, workflows, or applications.


How to Find Bacterial Genome Data on NCBI




There are several ways to find bacterial genome data on NCBI. Here are some of the most common and convenient methods:


How to use the Genome database to search for bacterial genomes by organism name, taxonomy, assembly level, etc.




The Genome database is a collection of complete and partial genome assemblies from various organisms. You can use it to search for bacterial genomes by various criteria, such as organism name, taxonomy, assembly level, bioproject, biosample, etc. You can also filter the results by organism group, assembly status, refseq category, etc.


Download bacterial genome sequence data from GenBank


Download bacterial genome annotation from Ensembl Bacteria


Download bacterial genome assembly from Wellcome Sanger Institute


Download bacterial genome comparison tools


Download bacterial genome browser software


Download bacterial genome alignment files


Download bacterial genome phylogeny trees


Download bacterial genome metabolic pathways


Download bacterial genome plasmid maps


Download bacterial genome resequencing data


Download bacterial genome editing tools


Download bacterial genome visualization tools


Download bacterial genome functional analysis tools


Download bacterial genome expression data


Download bacterial genome transcription factor binding sites


Download bacterial genome operon predictions


Download bacterial genome regulatory networks


Download bacterial genome CRISPR-Cas systems


Download bacterial genome antibiotic resistance genes


Download bacterial genome virulence factors


Download bacterial genome horizontal gene transfer events


Download bacterial genome pan-genome analysis tools


Download bacterial genome core-genome analysis tools


Download bacterial genome accessory-genome analysis tools


Download bacterial genome strain typing tools


Download bacterial genome SNP detection tools


Download bacterial genome variant calling tools


Download bacterial genome quality control tools


Download bacterial genome statistics tools


Download bacterial genome clustering tools


Download bacterial genome ortholog detection tools


Download bacterial genome paralog detection tools


Download bacterial genome synteny analysis tools


Download bacterial genome gene prediction tools


Download bacterial genome gene ontology annotation tools


Download bacterial genome protein domain annotation tools


Download bacterial genome protein structure prediction tools


Download bacterial genome protein-protein interaction prediction tools


Download bacterial genome metabolic network reconstruction tools


Download bacterial genome metabolic flux analysis tools


Download bacterial genome metabolic modeling tools


Download bacterial genome biotechnology applications


Download bacterial genome synthetic biology tools


Download bacterial genome engineering tools


Download bacterial genome evolution analysis tools


Download bacterial genome population genetics tools


Download bacterial genome phylogenomics tools


To use the Genome database to search for bacterial genomes:


Go to [14](


  • Type your query in the search box or use the advanced search option.



  • Select "Bacteria" from the "Organism group" facet in the left-hand sidebar.



  • Select your desired filters from the other facets in the left-hand sidebar.



  • Click on the "Download Assemblies" button to open the download menu.



  • Select your preferred file type (genomic fasta, genomic gbff, feature table) and source database (GenBank or RefSeq).



  • Click on the "Download" button to download a single file containing all selected assemblies or click on the "Download individual files" link to download each assembly separately.



How to use the FTP site to browse and download bacterial genomes by directory structure, file format, etc.




The FTP site is a file transfer protocol server that allows users to download large data sets from NCBI. You can use it to browse and download bacterial genomes by directory structure, file format, etc. You can also use the FTP site to download pre-computed data sets, such as BLAST databases, annotation reports, protein clusters, etc.


To use the FTP site to browse and download bacterial genomes:


Go to [13](


  • Navigate to the "Bacteria" or "Bacteria_DRAFT" directory, depending on whether you want complete or draft assemblies.



  • Choose a subdirectory based on the first letter of the genus name of the bacterium you are interested in.