Genome Standards

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.

This topic has re-surfaced as SangerWB have been in contact with the Sanger Helminth group regarding future integration of their data.

They run a pipeline whereby there are 4 phases

1) Production (X months) - No Interest for WB 
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2) Finishing  (3 Months) - No Interest for WB
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3) Analysis   (3 months) - Depending on our criteria we could be interested here
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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 when the genome/gene set meets their standards 

The Helminth Co-ordinator is going to send some information regarding the standards they will be working to but these will be based on the paper "Genome Project Standards in a New Era of Sequencing" so this might be a good starting point for WormBase to base our list of criteria.....(It's not very detailed :( )

Discussion

expected number of genes

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).

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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.

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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"