################################################################################ README for ftp://ftp.ncbi.nlm.nih.gov/genomes/ Last updated: January 27, 2020 ################################################################################ ******************************************************************************** NOTIFICATION OF CHANGE: January 27, 2020 The Genus_species FTP directories will be moved to genomes/archive/old_refseq/ after February 1, 2020. BACKGROUND The NCBI Eukaryotic Genome Annotation Pipeline is now publishing annotated RefSeq genomes to the newly created annotation release (AR) directories on the FTP site under genomes/refseq. These directories have the following structure: ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq///annotation_releases The files for the latest annotation releases of the 580+ species annotated by the NCBI Eukaryotic Genome Annotation Pipeline have been added to genomes/refseq. On February 1, 2020, we will stop publishing annotation results to the older genus_species directories immediately under ftp://ftp.ncbi.nlm.nih.gov/genomes. After that time, you can get files for newly released annotations from the genomes/refseq/ directories as described above or from the ftp://ftp.ncbi.nlm.nih.gov/genomes/all/annotation_releases/ directories where we have organized the same data by taxonomy id. ftp://ftp.ncbi.nlm.nih.gov/genomes/all/annotation_releases// Beginning February 1, 2020, we will move the existing ftp://ftp.ncbi.nlm.nih.gov/genomes/ directories to ftp://ftp.ncbi.nlm.nih.gov/genomes/archive/old_refseq/. See this NCBI Insights post for more details: https://ncbiinsights.ncbi.nlm.nih.gov/2019/12/05/new-assem-downloads/ Please comment on the NCBI Insights post or write to suggest@ncbi.nlm.nih.gov if you have any questions or concerns. ******************************************************************************** ******************************************************************************** ********** Many directories under ftp://ftp.ncbi.nlm.nih.gov/genomes/ ********** ********* were moved on 02-DEC-2015 ********** Assembled genome sequence and annotation data for RefSeq genome assemblies is now being provided under: ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq On 02 December 2015 the old directories and files listed below were moved as indicated. Moved to ftp://ftp.ncbi.nlm.nih.gov/genomes/archive/old_refseq/ The content of these directories will not be updated. Aedes_aegypti Anopheles_gambiae Arabidopsis_lyrata Arabidopsis_thaliana ASSEMBLY_BACTERIA Bacteria Bacteria_DRAFT Branchiostoma_floridae Caenorhabditis_elegans Chloroplasts CLUSTERS Drosophila_melanogaster Drosophila_pseudoobscura Fungi Medicago_truncatula MITOCHONDRIA Physcomitrella_patens PLANTS Plasmids Populus_trichocarpa Protozoa Sorghum_bicolor Moved to ftp://ftp.ncbi.nlm.nih.gov/genomes/archive/ old_genomeID2nucGI Moved to ftp://ftp.ncbi.nlm.nih.gov/genomes/GENOME_REPORTS/ IDS ******************************************************************************** ******************************************************************************** NOTIFICATION OF CHANGE: August 21, 2014 & August 3, 2015 ----------------------------------- Assembled genome sequence and annotation data is now comprehensively provided in three new directories: all, genbank, and refseq. Data are provided for all current assemblies available in NCBI's Assembly resource (www.ncbi.nlm.nih.gov/assembly) using standardized file names. The initial August 2014 release, and the February & August 2015 updates, include various data formats including fasta, GenBank and GenPept flat file, and GFF. RepeatMasker results are provided for eukaryotic genomes. A file with md5checksums is also provided for each assembly. ******************************************************************************** ======================= Background Information: ======================= The genomes FTP site provides sequence, annotation, and meta-data for all sequenced and assembled genomes that are available in NCBI's Assembly resource in addition to select additional project-oriented datasets. Annotation data is provided when available for assemblies that have been submitted to the International Nucleotide Sequence Database Collaboration (INSDC) including NCBI's GenBank database. RefSeq genomes are a subset of the genomes available in INSDC and all include annotation, except for some viruses. RefSeq annotation content originates from NCBI's prokaryotic, eukaryotic, organelle, or viral annotation pipelines, or is propagated from the GenBank submission. Available by anonymous FTP at: ftp://ftp.ncbi.nlm.nih.gov/genomes/ Please refer to README files and the FTP FAQ for additional information: https://www.ncbi.nlm.nih.gov/genome/doc/ftpfaq/ Subscribe to the genomes-announce mail list to be informed of changes to the NCBI genomes FTP site: https://www.ncbi.nlm.nih.gov/mailman/listinfo/genomes-announce ===================== Directory structure: ===================== Comprehensive reports of sequence and annotation data for assembled genomes (that are available in NCBI's Assembly resource) are provided in three directory areas: Genome sequence and annotation data: ------------------------------------ 1) all: content is the union of GenBank and RefSeq assemblies. Two directories under "all" are named for the accession prefix (GCA or GCF) and these directories contain another three levels of directories named for digits 1-3, 4-6 & 7-9 of the assembly accession. The next level is the data directories for individual assembly versions. Only data directories for "latest" assemblies are refreshed when annotation is updated or when software updates are released, so new file formats or improvements to existing formats are not available for non-latest assemblies. A third directory, named "annotation_releases" contains the products of the NCBI Eukaryotic Genome Annotation Pipeline. The data are organized first by taxonomy ID and then by annotation release ID. It is expected that many users will prefer to access the annotation release data using the paths under the "refseq" directory that use the organism name. 2) genbank: content includes primary submissions of assembled genome sequence and associated annotation data, if any, as exchanged among members of the International Nucleotide Sequence Database Collaboration, of which NCBI's GenBank database is a member. The GenBank directory area includes genome sequence data for a larger number of organisms than the RefSeq directory area; however, some assemblies are unannotated. The sub-directory structure includes: a. archaea b. bacteria c. fungi d. invertebrate e. metagenomes f. other - this directory includes synthetic genomes g. plant h. protozoa i. vertebrate_mammalian j. vertebrate_other k. viral 3) refseq: content includes assembled genome sequence and RefSeq annotation data. All prokaryotic and eukaryotic RefSeq genomes have annotation. RefSeq annotation data may be calculated by NCBI annotation pipelines or propagated from the GenBank submission. The RefSeq directory area includes fewer organisms than the GenBank directory area because not all genome assemblies are selected for the RefSeq project. Sub-directories include: a. archaea b. bacteria c. fungi d. invertebrate e. plant f. protozoa g. vertebrate_mammalian h. vertebrate_other i. viral j. mitochondrion [Content of the mitochondrion, plasmid and plastid k. plasmid directories is from the RefSeq release FTP site. See l. plastid ftp://ftp.ncbi.nlm.nih.gov/refseq/release/README] See ftp://ftp.ncbi.nlm.nih.gov/genomes/all/README.txt for a more detailed description of the organization of these directories, the data provided per assembly and a description of the files. Additional directories: ----------------------- Meta-data related to the Assembly and Genome resources are available here: 1) ASSEMBLY_REPORTS: content consists of four summary report files that include meta-data details of all the latest GenBank assemblies, all the latest RefSeq assemblies, the historical GenBank assemblies, or the historical RefSeq assemblies. These summary files provide a ftp path that can be used to retrieve the sequence and annotation data. assembly_summary_genbank.txt assembly_summary_genbank_historical.txt assembly_summary_refseq.txt assembly_summary_refseq_historical.tx ANI_report_bacteria.txt provides data on the Average Nucleotide Identity (ANI) between the latest version of prokaryote genome assemblies and the best matching type strain genome assembly. Another file, species_genome_size.txt.gz, provides the expected genome assembly size range for different species as applied to submissions to GenBank. Reports are provided by the Assembly resource: www.ncbi.nlm.nih.gov/assembly/ 2) GENOME_REPORTS: content consists of summary reports of genome sequencing projects, associated annotation statistics, and some defined reference datasets within the RefSeq project. Reports are provided by the Genomes resource: www.ncbi.nlm.nih.gov/genomes/ Several directories are also provided for other data groups including: INFLUENZA: sequence and annotation of INSDC influenza viruses HUMAN_MICROBIOM: sequence, annotation, and meta-data from the Human Microbiome Project (HMP) TARGET: sequence data from the RefSeq rRNA project TOOLS: select genomic tools Viruses: sequence and annotation of RefSeq viral genomes ________________________________________________________________________________ National Center for Biotechnology Information (NCBI) National Library of Medicine National Institutes of Health 8600 Rockville Pike Bethesda, MD 20894, USA tel: (301) 496-2475 fax: (301) 480-9241 e-mail: info@ncbi.nlm.nih.gov ________________________________________________________________________________