Genome Standards

Overview

This is the list of criteria that must be satisfied by a new genome assembly/project in order for us to accept it for integration into WormBase

We are happy to accept data pre-publication so that we can prepare it ready for adding to the database when you publish.

Requirements

Keep us informed of your progress

Contact us at help@wormbase.org early on in your project. We can then advise you about details and be prepared for your data when you publish it.

We like to be informed of upcoming genome submissions as early as possible, for example a typical lab that has contributed data is the Sanger Helminth group

They run a pipeline whereby there are 4 phases, we would normally integrate the data after their fourth phase

1) Production (X months) - No Interest for Wormbase
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2) Finishing  (3 Months) - No Interest for Wormbase
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3) Analysis   (3 months) - Wormbase are interested from this stage on - contact us at help@wormbase.org
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2') Repeat - Finishing
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3') Repeat - Analysis
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      x n (This means that it can go through several rounds before it is published)
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4) Publish and submit to ENA/GenBank when the genome/gene set meets their standards
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   Confirm it meets the Wormbase standards for integration, add to Wormbase.

Submission to INSDC

Our minimal requirement is that the genome assembly (bottom-level genomic sequences, and higher-level structure) should have been deposited with the one of the collaborating partners of the International Nucleotide Sequence Database Collaboration (www.insdc.org). We can then easily extract the data from the public archives and have confidence that assembly ise regarded as reasonably stable by the authors.

Gene models

We prefer you to do some prediction of the gene models in your genome.

All gene models should be at least 3 amino acids in length - mainly for Blast analysis as this is the minumum word size.

Gene models should translate into orthodox proteins (no stop codons or partial codons)

Minimum N50

We do not require a minimum N50. If you are happy for your data to be publicly available from the ENA/GenBank database, then we will consider including it in WormBase, but we reserve the right to reject genomes that are too fragmented for us to be able to load into our data structures.

Meta data

When writing to help@wormbase.org to tell us about the new genome assembly that you would like included in WormBase, it would be helpful to include the following information:

Handle to assembly in public reposiroties

This could be one (or both) of:

• An INSDC accession number;
• A direct link to the data under the NCBI genome FTP portal

Assembly statistics

As much information as you have available, but minimally the stage which your assembly project has reached - one of:

• Standard Draft
• High-Quality Draft
• Improved High-Quality Draft
• Annotation-Directed Improvement
• Noncontiguous Finished
• Finished

These stages are defined in the paper "Genome Project Standards in a New Era of Sequencing"

Provenance

• Species name
• Strain ID (preferrably the CGC strain ID)
• Origin of the Strain
• Some references describing the species

Attribution

• Primary Data Contact:
• Primary Data Contact Email:
• Project URL:
• FTP Site:
• Citation:

Submitted of annotation

If the gene models and other annotation have been deposited with an INSDC partner along with the genome sequence, there will be no need to submit any additional files direct to WormBase. However, we do appreciate that it is sometimes not possible to deposit the annotation in this way (either for technical reasons, or due to the requirement for embargo until publication).

We are therefore happy to accept direct submissions of annotation in GFF2 or GFF3.

TODO: Specify precise GFF2/GFF3 required (structure, source/type fields etc) for automatic flow into WormBase. Filenames less important.