Submit Annotated Sequence Flatfiles with Webin-CLI¶

Introduction¶

Annotated sequence flat files can be submitted to the European Nucleotide Archive (ENA) using the Webin command line submission interface with -context sequence option.

An annotated sequence submission consists of:

General sequence information
- Study accession or unique name (alias)
- Unique name for the submission
- Free text description of the submitted sequences (optional)
Sequences in EMBL-Bank flat file format

The following picture illustrates the stages of the annotated sequence flat file submission process:

../../_images/webin-cli_03.png Submission process

Stage 1: Pre-register study¶

Each submission must be associated with a pre-registered study.

Register a study

Stage 2: Prepare the files¶

The set of files that are part of the submission are specified using a manifest file. The manifest file is specified using the -manifest <filename> option.

An annotated sequence flat file submission consists of the following files:

1 manifest file
1 flat file containing the sequences and functional annotation

Manifest file¶

The manifest file has two columns separated by a tab (or any whitespace characters):

Field name (first column): case insensitive field name
Field value (second column): field value

The following metadata fields are supported in the manifest file:

STUDY: Study accession or unique name (alias)
NAME: Unique name for the submission
DESCRIPTION: Free text description of the submitted sequences (optional)

The following file name fields are supported in the manifest file:

FLATFILE: sequences in EMBL-Bank flat file format

For example, the following manifest file represents a submission:

STUDY   TODO
NAME   TODO
FLATFILE    sequences.dat.gz

Stage 3: Validate and submit the files¶

Files are validated, uploaded and submitted using the Webin command line submission interface. Please refer to the Webin command line submission interface documentation for more information about the submission process.

Assigned accession numbers¶

Once the sequences have been submitted an analysis (ERZ) accession number is immediately assigned and returned to the submitter by the Webin command line submission interface.

The purpose of the ERZ accession number is for the submitter to be able to refer to their submission within the Webin submission service. For example, the submitter can retrieve the assigned sequence accessions from the Webin submissions portal or from the Webin reports service using the ERZ accession number.

For sequences, long term stable accession numbers that can be used in publications are:

Study accession (PRJ) assigned at time of study registration.
Sequence accession(s) assigned once the submission has been fully processed by ENA.

Submitters can retrieve the sequence accession numbers from the Webin submissions portal or from the Webin reports service. These accession numbers are also send to the submitters by e-mail.