Download genome genbank

Tab-delimited text file reporting the name, role and sequence accession. The file header contains meta-data for the assembly including: assembly name, assembly accession.

Tab-delimited text file reporting statistics for the assembly including: total length, ungapped length, contig scaffold counts, contig-N50, scaffold-L50, scaffold-N50, scaffold-N75 scaffold-N Provided for assemblies that include alternate or patch assembly units.

Other files define how scaffolds and chromosomes are organized into non-nuclear and other assembly-units, and how any alternate or patch scaffolds are placed relative to the chromosomes. Only present if the assembly has internal structure. Tab-delimited text file reporting locations and attributes for a subset of annotated features. Replaces the. FASTA format of the genomic sequence s in the assembly.

Repetitive sequences in eukaryotes are masked to lower-case. The genomic. GenBank flat file format of the genomic sequence s in the assembly. Sequence identifiers are provided as accession. Annotation of the genomic sequence s in Gene Transfer Format Version 2. Tab-delimited text file reporting the coordinates of all gaps in the top-level genomic sequences. The gaps reported include gaps specified in the AGP files, gaps annotated on the component sequences, and any other run of 10 or more Ns in the sequences.

Documentation of the RepeatMasker version, parameters, and library text format ; Provided for eukaryotes. GenBank flat file format of the WGS master for the assembly present only if a WGS master record exists for the sequences in the assembly. Tab-delimited text file reporting hash values for different aspects of the annotation data. The hashes are useful to monitor for when annotation has changed in a way that is significant for a particular use case and warrants downloading the updated records.

Assembly directories for RefSeq genomes annotated by the NCBI Eukaryotic Genome Annotation Pipeline include extra sub-directories and files in additon to the standard set of files and formats. FASTA format of the genomic sequence corresponding to pseudogene and other gene regions which do not have any associated transcribed RNA products or translated protein products.

It includes annotated gene regions that require rearrangement to provide the final product, e. These sequences are not assigned accession numbers, and are derived directly from the assembled genomic sequences. These alignments may have been used as evidence for gene prediction by the annotation pipeline.

These alignments were used as evidence for gene prediction by the annotation pipeline. These identifiers are NOT universally unique. They are unique per annotation release only. Matching genes and transcripts in the current and previous annotation releases binned by type of difference column 1 for genes and column 14 for transcripts , in tabular format.

Genome Workbench project file for visualization and search of differences between the current and previous annotation releases. Each annotation release corresponds to an annotation run. The annotation release identifiers AR are numbered sequentially starting at , independently of the assembly used.

An assembly may have been annotated multiple times, and be featured in different annotation release directories. The 'current' directory contains the data for the most recent annotation. For many organisms, only the most recent annotation may be available. This file provides information specific to the specific annotation release, including data freeze dates, release date and release number, and the annotated assemblies.

It contains information on the annotation release, including: Important dates associated with the annotation Assemblies Gene and feature statistics Masking results Transcript and protein alignments used for the annotation Assembly-assembly alignments used to track genes from the previous assembly to the current, or from the reference to an alternate assembly if relevant Assembly directory One directory for each genome assembly that was annotated in the release.

Named as [assembly accession. This directory contains the files provided for all genome assemblies plus those additional files provided for organisms annotated by the NCBI Eukaryotic Genome Annotation Pipeline. GenBank Data Usage The GenBank database is designed to provide and encourage access within the scientific community to the most up-to-date and comprehensive DNA sequence information.

Confidentiality Some authors are concerned that the appearance of their data in GenBank prior to publication will compromise their work. Disclaimer Privacy statement. You are here: NCBI. External link. Please review our privacy policy. Released: Dec 1, View statistics for this project via Libraries.

However, Mick's scripts are written in Perl specific to actually building a Kraken database as advertised. Alternatively, ncbi-genome-download is packaged in conda. At the moment, this means versions 3. Specifically, no attempt at testing under Python versions older than 3.

If your system is stuck on an older version of Python, consider using a tool like Homebrew to obtain a more up-to-date version. Note : To see all available groups, see ncbi-genome-download --help , or simply use all to check all groups.

Naming a more specific group will reduce the download size and the time needed to find the sequences to download. If you're on a reasonably fast connection, you might want to try running multiple downloads in parallel:.

It is possible to download multiple formats by supplying a list of formats or simply download all formats:. Note : The quotes are important.

Again, this is a simple string match on the organism name provided by the NCBI. Then, pass the path to that file e. You can make the string match fuzzy using the --fuzzy-genus option. This can be handy if you need to match a value in the middle of the NCBI organism name, like so:. Note : The above command will download all bacterial genomes containing "coelicolor" anywhere in their organism name from RefSeq. Note : The above command will download all RefSeq genomes belonging to Escherichia coli.

Note : The above command will download the RefSeq genome belonging to Escherichia coli str. K substr. It is also possible to download multiple species taxids or taxids by supplying the numbers in a comma-separated list:.

In addition, you can put multiple species taxids or taxids into a file, one per line and pass that filename to the --species-taxids or --taxids parameters, respectively. It is possible to also create a human-readable directory structure in parallel to mirroring the layout used by NCBI:.

You can update this database by using the --update flag. Note that if the database is not in your home directory, you must specify it with --database or a new database will be created in your home directory. Skip to content. Star Branches Tags. Could not load branches. Could not load tags. Latest commit. Git stats commits. Failed to load latest commit information. View code. So this is a set of scripts that focuses on the actual genome downloading.

Installation pip install ncbi-genome-download. Streptomyces Amycolatopsis. Releases 12 Release 0. Dec 1,