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What means "high quality" reference genome

Hello,

I'm new to Bioinformatics, just starting my second year, and there is a question I can't find a clear answer:

Some papers uses the term of "high quality reference genome". I know what is a reference genome, but what does scientists call a "high quality"? What differs from a standard one ?

If anyone could enlighten me I would be grateful.

genome sequence
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updated by GenoMax GenoMax • written by aeringw • aeringw

3 answers

Genome finishing standards were defined in this publication.

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written by GenoMax GenoMax

A high quality reference genome would be the mouse or human genome. In general, this is a reference genome with relatively few gaps and very thorough gene/repeat/etc. annotations.

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written by Devon Ryan Devon Ryan

I'll just add that this term is used very loosely nowadays and people consider their genome rather quickly/easily to be "high quality"

other examples of high quality genomes: yeast, arabidopsis, ... (often those genomes that date back to the pre-NGS era )

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written by lieven.sterck lieven.sterck

Anyone can sequence a genome, run an assembly tool and call it a reference genome. The difference with a high quality reference genome is in filling gaps and correcting mis-assemblies. This is often called "finishing" a reference genome and may involve other techniques (sequencing BAC clones, using long read sequencing data, bionano genomics, etc) and manual curation.

Especially "next-generation sequencing" like Illumina results in highly fragmented genome assemblies with many contigs and gaps, since their read length is short. Older assemblies, such as Drosophila, Mouse, Human were initially created using Sanger sequencing.

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written by WouterDeCoster WouterDeCoster

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