Difference between revisions of "Genome Standards"
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| − | + | = Overview = | |
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| − | + | '''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''' | |
| − | + | = 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. | |
| − | + | == Submission to INSDC == | |
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| − | + | 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 [http://www.insdc.org www.insdc.org]. We can then easily extract the data from the public archives and have confidence that assembly is regarded as reasonably stable by the authors. | |
| + | WormBase can offer advice/help on how to go about doing this. | ||
| − | == | + | == Assembly quality == |
| − | + | We do not have an official threshold on assembly quality, e.g. 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. | |
| − | + | == Gene models == | |
| − | + | You should provide a canonical gene set with your genome sequence. Without a gene set, we cannot include your species in our orthology infererence pipelines, resulting in only limited integration with the other species in WormBase. | |
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| − | |||
| − | + | 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). In those cases, we will therefore consider direct submissions of annotation in [http://www.sequenceontology.org/gff3.shtml GFF3]. We encourage authors to contact us in advance of the preparation of the files so that we can advise on content and form. | |
| − | + | === Sanity checks === | |
| − | + | We apply the following sanity checks on gene models; any models failing these checks are excluded | |
| − | + | ==== Translation ==== | |
| − | + | Protein-coding models should translate into orthodox proteins (no stop codons or partial codons) | |
| − | + | ==== Minimum length ==== | |
| − | + | Protein-coding gene models should be at least 3 amino acids in length. This restriction is mainly for BLAST analysis (as this is the minimum word size), but prevents other problem too. | |
| + | == Identifiers == | ||
| + | If your genome assembly and annotation has been deposited with INSDC, we will use the INSDC identifiers, as these are guaranteed to be globally unique. If the submission is pending, and accessions are not yet available, WormBase may take the liberty of renaming your objects on initial submission, to ensure that they are globally unique within our database. | ||
| − | === | + | If re-submitting a new/updated version of data for a species that we already have in WormBase, care must be taken with identifiers, particularly those of the genes, transcripts and proteins. If possible, you should ensure that identifiers are propagated forward to new versions of the annotation, such that a specific gene (for example) retains the same identifier. Without this, users may have trouble migrating their work on a given species to the new data. |
| + | |||
| + | == 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 [ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/invertebrates 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 [http://www.sciencemag.org/cgi/content/full/326/5950/236#R2 "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 | ||
| + | * Citation | ||
| + | |||
| + | |||
| + | [[Category:User Guide]] | ||
| + | [[Category:Curation]] | ||
Latest revision as of 09:02, 22 May 2012
Contents
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
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.
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 is regarded as reasonably stable by the authors.
WormBase can offer advice/help on how to go about doing this.
Assembly quality
We do not have an official threshold on assembly quality, e.g. 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.
Gene models
You should provide a canonical gene set with your genome sequence. Without a gene set, we cannot include your species in our orthology infererence pipelines, resulting in only limited integration with the other species in WormBase.
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). In those cases, we will therefore consider direct submissions of annotation in GFF3. We encourage authors to contact us in advance of the preparation of the files so that we can advise on content and form.
Sanity checks
We apply the following sanity checks on gene models; any models failing these checks are excluded
Translation
Protein-coding models should translate into orthodox proteins (no stop codons or partial codons)
Minimum length
Protein-coding gene models should be at least 3 amino acids in length. This restriction is mainly for BLAST analysis (as this is the minimum word size), but prevents other problem too.
Identifiers
If your genome assembly and annotation has been deposited with INSDC, we will use the INSDC identifiers, as these are guaranteed to be globally unique. If the submission is pending, and accessions are not yet available, WormBase may take the liberty of renaming your objects on initial submission, to ensure that they are globally unique within our database.
If re-submitting a new/updated version of data for a species that we already have in WormBase, care must be taken with identifiers, particularly those of the genes, transcripts and proteins. If possible, you should ensure that identifiers are propagated forward to new versions of the annotation, such that a specific gene (for example) retains the same identifier. Without this, users may have trouble migrating their work on a given species to the new data.
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
- Citation
