Difference between revisions of "Genome Standards"

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We can then easily extract the data from the public databases and the assembly will be regarded as reasonably stable by the authors.
 
We can then easily extract the data from the public databases and the assembly will be regarded as reasonably stable by the authors.
  
=== Expected number of genes ===
+
=== Gene model prediction ===
  
We like to have your estimate of the number of geens in the genome.
+
We prefer you to do some prediction of the gene models in your genome.
 +
 
 +
If prediction gene models is not possible, we would like to have your estimate of the number of genes in the genome.
  
 
To get an estimated of how many genes could be expected in an assembly, you could take the average gene length and see how many can be at maximum being predicted based on the available contigs (if you can come up with the intergenic percentage you can include that). Take this in correlation to a wild guess on the gene number (like 20k) and you got a % completeness (and a huge error bar).
 
To get an estimated of how many genes could be expected in an assembly, you could take the average gene length and see how many can be at maximum being predicted based on the available contigs (if you can come up with the intergenic percentage you can include that). Take this in correlation to a wild guess on the gene number (like 20k) and you got a % completeness (and a huge error bar).

Revision as of 10:13, 18 May 2011

WormBase Genome Integration Standards

Overview:

This is the list of criteria that a genome assembly/project should attain before WormBase can agree to integrate the Organism into the database.

Submission of genomes to the Wormbase database is a common requirement. This document is a guide for this who wish their nematode genomes to be included in Wormbase.

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

Requirements

Submission to ENA/GenBank

Normally we expect the genome to be submitted to the public nucleotide databases.

We can then easily extract the data from the public databases and the assembly will be regarded as reasonably stable by the authors.

Gene model prediction

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

If prediction gene models is not possible, we would like to have your estimate of the number of genes in the genome.

To get an estimated of how many genes could be expected in an assembly, you could take the average gene length and see how many can be at maximum being predicted based on the available contigs (if you can come up with the intergenic percentage you can include that). Take this in correlation to a wild guess on the gene number (like 20k) and you got a % completeness (and a huge error bar).


WormBase Standards Document

Assembly statisitics

Standard Draft:

High-Quality Draft:

Improved High-Quality Draft:

Annotation-Directed Improvement:

Noncontiguous Finished:

Finished:

Attribution

Added by TH. Totally ad-hoc, but we should capture some information on who to contact so that we can display this on the species pages.

Primary Data Contact:

Primary Data Contact Email:

Project URL:

FTP Site:

Citation:

Gene Models

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



Minimum Standards

  • Submission to a public Nucleotide Repository
  • Wiki description of the Species, submitted by data producer if possible.
  • N50 of ?

Core Files

Data should be provided in standardized formats using the following conventions

  • Genomic Sequence
File format : FASTA
File name   :
  • Conceptual transcripts (spliced)
File format : FASTA
File name   :
  • Conceptual transcripts (unspliced)
File format :
File name   : g_species.gff2
  • Conceptual translations
File format : FASTA
File name   :
  • Genomic Features
File format :
File name   : g_species.gff2

See Also

The Helminth Co-ordinator discusses some requirements for submitting genomes in the paper "Genome Project Standards in a New Era of Sequencing"