Read domain formats

This page provides information on the read domain formats in ENA. If you are planning to submit read data into ENA, please refer first to Submitting read data.

Read data format

Read data including bases, base qualities and alignments can be submitted in several different formats ... more information.

Read metadata format

Metadata is represented using XML documents. For detailed information about the metadata XMLs please refer to the XML 1.5 metadata format. For examples how to prepare the XMLs please refer to Preparing XMLs. The following metadata objects are used:

Metadata object Description Example
Study A study groups together data submitted to the archive. Please use the study accession number when citing data submitted into ENA. ERP000016
Submission A submission contains submission actions to be performed by the archive. A submission can add more objects to the archive, update already submitted objects or make objects publicly available. ERA000092
Sample A sample contains information about the sequenced samples. Samples are associated with checklists, which define the attributes used to annotate the samples, and experiments or analysis objects. ERS000081
Experiment An experiment contains information about the sequencing experiments including library and instrument detail. ERX000398
Run Runs are part of experiments and contain sequencing reads submitted in data files (e.g. BAM or CRAM). Each run can contain all or part of the results for a particular experiment. ERR003990
Analysis An analysis contains secondary analysis results computed from the primary sequencing results (e.g. VCFs with sequence variations or BAMs with sequence alignments). ERZ000001
DAC An European Genome-phenome Archive (EGA) data access committee (DAC). Required for authorized access submissions. EGAC00001000001
Policy An European Genome-phenome Archive (EGA) data access policy. Required for authorized access submissions. EGAP00001000001
Dataset An European Genome-phenome Archive (EGA) data set. Required for authorized access submissions. EGAD00001000001

Accession number format

Each metadata object is assigned a unique accession number by the archive. The accession numbers can be used to retrieve data and metadata using the EB-Eye search available at the top of all EBI web pages or using the free text search available on the ENA home page. The metadata is then retrieved and displayed through the ENA Browser as in the examples in the above table.

Accession numbers assocaited with read data assigned by EBI start with 'ER' and accession numbers assigned by NCBI and DDBJ start with 'SR' and 'DR', respectively. The third letter of the accession number indicates the type of the metadata object. EGA accession numbers start with 'EGA' with the fourth letter indicating the type of the metadata object.

The accession numbers have a fixed number of digits after the letters: six for ENA and eleven for EGA.

Metadata object Accession prefix Number of digits Example
Submission ERA, SRA, DRA 6 ERA000092
Sample ERS, SRS, DRS 6 ERS000081
Study ERP, SRP, DRP 6 ERP000016
Experiment ERX, SRX, DRX 6 ERX000398
Run ERR, SRR, DRR 6 ERR003990
Analysis ERZ, SRZ, DRZ 6 ERZ000001
EGA Submission EGA 11 EGA00001000001
EGA Sample EGAN 11 EGAN00001000001
EGA Study EGAS 11 EGAS00001000001
EGA Experiment EGAX 11 EGAX00001000001
EGA Run EGAR 11 EGAR00001000001
EGA Analysis EGAZ 11 EGAZ00001000001
EGA DAC EGAC 11 EGAC00001000001
EGA Policy EGAP 11 EGAP00001000001
EGA Data Set EGAD 11 EGAD00001000001

Archive generated fastq file format

Once made public, data submitted to ENA are available for download using ftp and Aspara. Detailed data download instructions are available here. Currently, both submitted data files and archive generated fastq files are made available for download. The naming and format of the generated fastq files are described below.

In general, one fastq file is created for each application read in a run. Please refer to the table below for full details:

Number of application reads Fastq Files Description
1 <run accession>.fastq.gz For experiments with single application reads only all reads will be made available in one fastq file.
2 <run accession>_1.fastq.gz
<run accession>_2.fastq.gz
<run accession>.fastq.gz
For paired experiments with two application reads reads will be made available in 1-3 fastq files. If a paired experiment is submitted with both application reads then the first reads will be in <run accession>_1.fastq.gz file, the second reads will be in <run accession>_2.fastq.gz, and any unpaired reads will be in <run accession>.fastq.gz file. In case a paired experiment is submitted containing only unpaired reads then only a single file will be created: <run accession>.fastq.gz.
> 2 <run accession>_N.fastq.gz For experiments with more than two application reads (e.g. Complete Genomics or strobed PacBio) one fastq file is created for each application read, however, no empty fastq files are created.

The fastq file format is:

@<run accession>.<spot index>[ <spot name>\[/<read index>\]]
<bases>
+
<phred qualities, ASCII encoded starting with '!' (33)>
Field Description
<run accession> The Run accession. A spot is identified uniquely by the combination of the Run accession and the spot index.
<spot index> A positive integer assigned to the spots in the order in which they appear in the run. A spot is identified uniquely by the combination of the Run accession and the spot index.
<spot name> The spot name as it was provided by the submitter. In cases where the read name is missing or was removed by the archive this field is not present.
<read index> A positive integer assigned to the application reads in the order in which they appear in the spot: /1 for first application read and /2 for the second application read. In cases where the read name is missing or was removed by the archive this field is not present.

Examples

Single layout:

@ERR000017.1 IL6_554:7:1:249:322
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+
??????????????????????????????>>>>>>

 

Paired (first read):

@ERR005143.1 ID49_20708_20H04AAXX_R1:7:1:41:356/1
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+
hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh

 

Paired (second read):

@ERR005143.1 ID49_20708_20H04AAXX_R1:7:1:41:356/2
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+
hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh

 

Single layout without read names:

@ERR000017.1
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+
??????????????????????????????>>>>>>

 

Paired without read names (first read):

@ERR005143.1
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+
hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh

 

Paired without read names (second read):

@ERR005143.1
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+
hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh

 

SOLiD color:

The first base is included before the SOLiD colors.

@ERR000451.1 VAB_S0103_20080915_542_14_17_70_F3
T33023230203102103223330020300233001
+
T<.6353&:#$1%&(--27*%&%,

Latest ENA News

20 Aug 2014: Read data through Globus GridFTP
Read data can now be downloaded using Globus GridFTP through ebi#ena Globus Online public endpoint.

18 Aug 2014: Changes to SRA XML 1.5
Small changes to Experiment XML, Analysis XML, EGA Dataset XML, EGA DAC XMLs were deployed on 11th of August 2014.

1 Jul 2014: ENA release 120
Release 120 of ENA's assembled/annotated seqences now available

23 May 2014: Change to date format for advanced search
From 16th June 2014, the date format used in the advanced search will be changed to ISO format (YYYY-MM-DD).

20 May 2014: Update to the ENA SAMPLE checklist
From 10th of June 2014 the ENA SAMPLE checklist XML will be updated and the older version will be deprecated.