European Nucleotide Archive

https://ena-docs.readthedocs.io/en/latest/
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The European Nucleotide Archive (ENA) provides a comprehensive repository for nucleotide sequence...
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### Info File Example - ENA

Source: https://ena-docs.readthedocs.io/en/latest/submit/general-guide/webin-cli

Example of a separate info file used for backward compatibility in ENA submissions. This file contains metadata fields and must be referenced in the main manifest file using the `INFO` field.

```text
INFO	assembly.info
FASTA	genome.fasta.gz
```

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### Example Manifest File (Webin-CLI)

Source: https://ena-docs.readthedocs.io/en/latest/_sources/submit/sequence

Demonstrates the structure of a manifest file for Webin-CLI submissions. It requires STUDY and NAME fields, and optionally supports DESCRIPTION, FLATFILE, or TAB fields. FLATFILE and TAB are mutually exclusive.

```text
STUDY        todo
NAME         todo
FLATFILE     <filename>.embl.gz
```

```text
STUDY        todo
NAME         todo
TAB          <filename>.tsv.gz
```

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### Run Webin-CLI Java Jar

Source: https://ena-docs.readthedocs.io/en/latest/submit/general-guide/webin-cli

This snippet demonstrates how to execute the Webin-CLI program as a self-executing Java JAR file. It requires Java to be installed and specifies the JAR file path along with any necessary command-line options. The example shows variations for Mac/Linux and Windows operating systems.

```bash
java -jar webin-cli-<version>.jar <options>
java -jar webin-cli-1.7.3.jar <options>
# Example for Mac/Linux:
java -jar Downloads/webin-cli-1.7.3.jar <options>
# Example for Windows:
java -jar Downloads\webin-cli-1.7.3.jar <options>
```

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### Text Manifest File Example - ENA

Source: https://ena-docs.readthedocs.io/en/latest/submit/general-guide/webin-cli

Example of a text-based manifest file used for ENA submissions. This format uses tab-separated values to define metadata fields and file names. It's suitable for simpler submissions.

```text
STUDY	Study accession or unique name (alias)
SAMPLE	Sample accession or unique name (alias)
ANALYSIS_REF	Comma separated list of analysis accession(s) 
RUN_REF	Comma separated list of run accession(s)  

<file type>	<file name>

FASTA	genome.fasta.gz

STUDY	TODO
SAMPLE	TODO
ASSEMBLYNAME	TODO
COVERAGE	TODO
PROGRAM	TODO
PLATFORM	TODO
MINGAPLENGTH	TODO
MOLECULETYPE	genomic DNA
FASTA	genome.fasta.gz
```

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### Example Manifest File for Webin-CLI (Flatfile)

Source: https://ena-docs.readthedocs.io/en/latest/submit/sequence

This example demonstrates the structure of a manifest file for sequence submission using a flat file. It includes mandatory fields STUDY and NAME, and the FLATFILE field pointing to the sequence data file.

```text
STUDY        todo
NAME         todo
FLATFILE     <filename>.embl.gz

```

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### Using Aspera for Webin-CLI File Uploads

Source: https://ena-docs.readthedocs.io/en/latest/submit/general-guide/webin-cli

Specifying the use of the Aspera protocol for file uploads with Webin-CLI via the -ascp option. Requires Aspera CLI to be installed and its directory included in the system's PATH.

```shell
webin-cli-<version>.jar -ascp <options>
```

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### Manifest File Example for Binned Metagenome Assembly

Source: https://ena-docs.readthedocs.io/en/latest/_sources/submit/assembly/metagenome/binned

An example of a manifest file used for binned metagenome assembly submissions. It specifies required metadata fields and the location of the FASTA file containing the sequences. Fields are tab-separated.

```text
STUDY	TODO
SAMPLE	TODO
RUN_REF	TODO
ASSEMBLYNAME	TODO
ASSEMBLY_TYPE	TODO
COVERAGE	TODO
PROGRAM	TODO
PLATFORM	TODO
MINGAPLENGTH	TODO
MOLECULETYPE	genomic DNA
FASTA	binned_metagenome.fasta.gz
```

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### Webin-CLI Advanced Submission Options

Source: https://ena-docs.readthedocs.io/en/latest/submit/general-guide/webin-cli

These options provide advanced control over the Webin-CLI submission process, such as using a test service, enabling Aspera CLI for faster transfers, and retrieving program version or help information. These are useful for testing and optimizing submissions.

```bash
# Advanced options:
-test
-ascp
-version
-help
```

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### Sequence Record FASTA Example

Source: https://ena-docs.readthedocs.io/en/latest/_sources/submit/analyses/taxonomic-reference-set

Example format for sequence records within a multi-FASTA file for Taxonomic Reference Sets. Each record starts with an ID line, which must uniquely identify the sequence and match an identifier in the sequence metadata table. Additional details can be appended after a '|'.

```fasta
>ITS1DB00588027|162468|Steinernema abbasi|ITS1 located by ENA annotation, 267bp
ATCGactgRYSWKMBDHVryswkmbdhvNn
```

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### Webin-CLI Submission Command Example

Source: https://ena-docs.readthedocs.io/en/latest/submit/analyses/taxonomic-reference-set

An example command for using the Webin-CLI tool to validate or submit sequence metadata. This command requires username, password, context, and manifest file path. It includes options for validation or submission, and an optional test server flag.

```bash
webin-cli -username Webin-99999 -password xxxxxx -context taxrefset -manifest trs_submission.txt -validate
```

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### Example BioProject Accession XML - ENA

Source: https://ena-docs.readthedocs.io/en/latest/_sources/submit/study/programmatic

This XML snippet demonstrates how a BioProject accession number, typically starting with 'PRJEB', is presented in the ENA submission receipt. It includes attributes like accession, alias, and status.

```xml
<PROJECT accession="PRJEB20767" alias="cheddar_cheese" status="PRIVATE" />
```

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### Example Submission XML for Adding Objects

Source: https://ena-docs.readthedocs.io/en/latest/_sources/submit/analyses/sequence-annotation

This is a basic Submission XML file used to instruct ENA on actions to take. The example shows the `<ADD/>` action, indicating that new objects should be submitted.

```xml
<SUBMISSION>
   <ACTIONS>
      <ACTION>
         <ADD/>
      </ACTION>
   </ACTIONS>
</SUBMISSION>
```

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### Show Help for enaDataGet Command

Source: https://ena-docs.readthedocs.io/en/latest/_sources/retrieval/programmatic-access/browser-tools

Displays the available arguments and usage instructions for the `enaDataGet` command. This is useful for understanding the command's capabilities and options before downloading data. No specific inputs are required other than the command itself.

```bash
> enaDataGet --help
```

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