Different qualities of genomes - Is there a standard/definition?
2
1
Entering edit mode
8.7 years ago
mschmid ▴ 180

There are different terms for the quality/status of a genome assembly. Like "draft genome", "finished genome" or "high quality genome".

For the case of bacteria I am interested in any standard/"official" definition of quality standards. I basically understand the meaning of the definitions above. But I would like to have a source where I can find an overview of this kind of definitions (what else is commonly used?) and what they are supposed to describe. As already stated, I am mainly dealing with bacteria, so the definitions would ideally apply to bacteria.

genome • 2.2k views
ADD COMMENT
5
Entering edit mode
8.7 years ago
Fidel ★ 2.0k

Check the Sequence ontology. They have a controlled vocabulary for the qualities of the genomes.

For the term 'whole_genome_sequence_status' you find definitions for the following children:

noncontiguous_finished (SO:0001490)
high_quality_draft (SO:0001487)
standard_draft (SO:0001486)
improved_high_quality_draft (SO:0001488)
finished_genome (SO:0001491)
annotation_directed_improved_draft (SO:0001489)
ADD COMMENT
1
Entering edit mode
8.7 years ago
GenoMax 141k

See this paper from Science: https://www.sciencemag.org/content/326/5950/236.full Authors include people who primarily work with bacteria so the definitions should be applicable widely.

ADD COMMENT

Login before adding your answer.

Traffic: 1281 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6