ENA FTP Structure

The root of the ENA FTP server is at:

ftp://ftp.ebi.ac.uk/pub/databases/ena/

This server contains short pieces of assembled/annotated sequence dating back to the early 80s, as well as larger scale data types including genome assemblies, MAG/SAG assemblies, and transcriptome sequence assemblies. This server does not contain other data types such as raw reads, which can be found in the SRA FTP server.

It is expected that users will find relevant data through the various search interfaces available from ENA, rather than directly interacting with and navigating the FTP server. This page therefore does not provide an exhaustive explanation of the server’s structure, but serves to briefly describe what you will find in some of its most important subdirectories.

For some, but not all categories, suppressed data is kept separate from public.

Most data is available in EMBL flat file format, with some also available as FASTA.

Doc
Information on the INSDC feature table format, with versions dating back to 1995
Genome Collections
An XML file containing cumulative information on all genome collection accessions
Assembly
Plaintext reports on the content of genome assemblies, organised by genome collection accession (GCA)
WGS
Whole genome shotgun contig-level assembly, one multi-record flatfile and one multi-FASTA file per sequencing project
TSA
Transcriptome shotgun assembly records, one multi-record flatfile and one multi-FASTA file per sequencing project
Sequence
Generalised sequence category, organised by sequence type and taxon class
Coding
Protein-coding sequences, organised by sequence type and accession number
Non-Coding
Non-protein-coding sequences, organised by sequence type and accession number
rRNA
Ribosomal RNA sequences, organised by sequence type and accession number
TLS
Targeted locus study sequences, one multi-record flatfile and one multi-FASTA file per sequencing project